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Full wwPDB EM Validation Report i○
Dec 14, 2020 – 11:55 PM JST
PDB ID : 5Y81EMDB ID : EMD-6816
Title : NuA4 TEEAA sub-complexAuthors : Wang, X.; Cai, G.
Deposited on : 2017-08-18Resolution : 4.70 Å(reported)
This is a Full wwPDB EM Validation Report for a publicly released PDB entry.
We welcome your comments at [email protected] user guide is available at
https://www.wwpdb.org/validation/2017/EMValidationReportHelpwith specific help available everywhere you see the i○ symbol.
The following versions of software and data (see references i○) were used in the production of this report:
EMDB validation analysis : 0.0.0.dev61MolProbity : 4.02b-467
Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)Ideal geometry (proteins) : Engh & Huber (2001)
Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : 2.15.1
Page 2 Full wwPDB EM Validation Report EMD-6816, 5Y81
1 Overall quality at a glance i○
The following experimental techniques were used to determine the structure:ELECTRON MICROSCOPY
The reported resolution of this entry is 4.70 Å.
Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.
Metric Whole archive(#Entries)
EM structures(#Entries)
Clashscore 158937 4297Ramachandran outliers 154571 4023
Sidechain outliers 154315 3826
The table below summarises the geometric issues observed across the polymeric chains and their fitto the map. The red, orange, yellow and green segments of the bar indicate the fraction of residuesthat contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. A greysegment represents the fraction of residues that are not modelled. The numeric value for eachfraction is indicated below the corresponding segment, with a dot representing fractions <=5%The upper red bar (where present) indicates the fraction of residues that have poor fit to the EMmap (all-atom inclusion < 40%). The numeric value is given above the bar.
Mol Chain Length Quality of chain
1 B 1115
2 C 336
3 D 500
4 H 279
5 A 2627
6 F 490
7 G 375
8 E 41
Page 3 Full wwPDB EM Validation Report EMD-6816, 5Y81
2 Entry composition i○
There are 8 unique types of molecules in this entry. The entry contains 25723 atoms, of which 0are hydrogens and 0 are deuteriums.
In the tables below, the AltConf column contains the number of residues with at least one atomin alternate conformation and the Trace column contains the number of residues modelled with atmost 2 atoms.
• Molecule 1 is a protein called Transcription-associated protein 1.
Mol Chain Residues Atoms AltConf Trace
1 B 981 Total C N O S5937 3675 1116 1136 10 0 0
• Molecule 2 is a protein called Chromatin modification-related protein EAF1.
Mol Chain Residues Atoms AltConf Trace
2 C 140 Total C N O S800 489 156 154 1 0 0
• Molecule 3 is a protein called Eaf1-disorder domain.
Mol Chain Residues Atoms AltConf Trace
3 D 360 Total C N O1800 1080 360 360 0 0
• Molecule 4 is a protein called Chromatin modification-related protein EAF5.
Mol Chain Residues Atoms AltConf Trace
4 H 154 Total C N O764 456 154 154 0 0
• Molecule 5 is a protein called Transcription-associated protein 1.
Mol Chain Residues Atoms AltConf Trace
5 A 2007 Total C N O10017 5997 2008 2012 0 0
• Molecule 6 is a protein called Actin-related protein 4.
Mol Chain Residues Atoms AltConf Trace
6 F 421 Total C N O S3334 2121 553 648 12 1 0
Page 4 Full wwPDB EM Validation Report EMD-6816, 5Y81
There is a discrepancy between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceF 0 PRO - expression tag UNP P80428
• Molecule 7 is a protein called Actin.
Mol Chain Residues Atoms AltConf Trace
7 G 351 Total C N O S2729 1735 458 519 17 0 0
• Molecule 8 is a protein called Chromatin modification-related protein EAF1.
Mol Chain Residues Atoms AltConf Trace
8 E 41 Total C N O S342 222 56 61 3 0 0
Page 5 Full wwPDB EM Validation Report EMD-6816, 5Y81
3 Residue-property plots i○
These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. Thefirst graphic for a chain summarises the proportions of the various outlier classes displayed in thesecond graphic. The second graphic shows the sequence view annotated by issues in geometry andatom inclusion in map density. Residues are color-coded according to the number of geometricquality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2and red = 3 or more. A red diamond above a residue indicates a poor fit to the EM map forthis residue (all-atom inclusion < 40%). Stretches of 2 or more consecutive residues without anyoutlier are shown as a green connector. Residues present in the sample, but not in the model, areshown in grey.
• Molecule 1: Transcription-associated protein 1
Chain B:
TYR
ASN
ALA
W263
3�
Y263
4Q2
635
S263
6�
I263
7N2
638
I263
9L2
640
E264
1S2
642
I264
3�
T264
7S2
648�
I264
9D2
650
N265
1T2
652
K265
3I2
654
I265
5E2
656
E265
9
L266
2L2
663
E266
4L2
665
Q267
0E2
671
M267
4F2
675
L267
8
R268
1
I269
0G2
691
E269
5Q2
696
I269
7GL
YLE
UW2
700
R271
5SE
RGL
YAL
ALE
UPR
OTY
R
SER
Q272
3
A273
7
L274
0GL
NHI
STR
PD2
744
V274
5L2
746
T274
7E2
748
H275
2
E276
1
R276
5V2
766
ALA
ASP
TRP
ASN
SER
ASP
R277
3
E277
7Q2
778
S277
9V2
780
K278
1S2
782
V278
3
P278
7T2
788
P278
9R2
790
R279
1Q2
792
F279
7
R280
7LY
SG2
809
C281
7D2
818
E281
9G2
820
I282
1Q2
822
L282
3S2
824
L282
5I2
826
K282
7W2
828
VAL
SER
LEU
PRO
ILE
R283
4Y2
835
T283
6P2
837
A283
8H2
839
K284
0W2
841
L284
2L2
843
H284
4G2
845
F284
6Q2
847
Q284
8Y2
849
M285
0E2
851
F285
2L2
853
E285
4A2
855
T285
6
T286
6�
VAL
GLN
ASN
LEU
ASP
SER
LYS
A287
4Q2
875
E287
6
Q288
2
R288
5D2
886
R288
7L2
888
P288
9AS
NTH
RTR
PAS
PD2
894
V289
5N2
896
M289
7W2
898
N289
9
D290
0L2
901
V290
2
Q290
6
I291
2N2
913
N291
4A2
915
P292
1A2
922
L292
3GL
NGL
NSE
RAS
NSE
RAS
NSE
RAS
NIL
EAS
NTH
RHI
SAL
ATY
RR2
938
H294
1E2
942
I294
3A2
944
W294
5V2
946
I294
7
H295
2
H295
7N2
958
D296
1V2
962
C296
3I2
964
S296
5Q2
966
L296
7A2
968
R296
9I2
970
Y297
1T2
972
LEU
PRO
ASN
ILE
GLU
ILE
GLN
E298
0�
C299
1
N299
7E2
998
L299
9T3
000�
T300
1
S300
7N3
008
THR
ASN
LEU
VAL
TYR
PHE
G301
5
K301
9A3
020
F302
3
L303
3AR
GAL
ATY
RGL
UE3
038
A303
9N3
040
Q304
1A3
042
F304
3A3
044
T304
5A3
046
V304
7
D305
0
L305
3A3
054
K305
5A3
056
W305
7A3
058
Q305
9W3
060
G306
1F3
062
F306
3N3
064
D306
5R3
066
R306
7
L306
8�
S306
9E3
070
E307
1P3
072
ASN
ASN
ILE
S307
6F3
077
A307
8
A308
1I3
082
Y308
5L3
086
A308
9
N309
4S3
095
K309
6I3
097
R309
8E3
099
L310
0L3
101
C310
2R3
103
I310
4L3
105
W310
6L3
107
I310
8S3
109
I311
0D3
111
G311
5M3
116
L311
7T3
118
N311
9
P312
9
I313
4�
T313
5F3
136
Q313
9L3
140
L314
1T3
142
S314
3L3
144
S314
5
A314
9
N315
0
I315
9A3
160
K316
1S3
162
Y316
3P3
164
Q316
5A3
166
L316
7H3
168
F316
9Q3
170
L317
1R3
172
T317
3T3
174
I318
1GL
NAR
GGL
NTH
RME
TAL
AVA
LME
TGL
YAS
PLY
SPR
OAS
PTH
RAS
NAS
PAR
GAS
NGL
YAR
GAR
GQ3
203
P320
4
T321
7A3
218
Y321
9P3
220
L322
1L3
222
A322
3
L322
9
R323
6
T324
1D3
242
E324
3D3
244
L324
5F3
246
R324
7L3
248
I324
9N3
250
V325
1L3
252
L325
3
P326
4PH
EPR
OAR
GLY
SAS
NPR
OLY
SLE
UP3
273
Y329
1I3
292
R329
3�
F329
6
F330
0IL
EAS
PAS
NLY
SPR
OAS
PY3
307
L331
4R3
315
Y331
6W3
317
R331
8
E332
2
R332
7AL
ASE
RLY
SLY
SGL
UAS
NLE
UGL
UVA
LLE
UC3
338
F334
4
F334
9�
E335
0�
D335
1�
I335
4P3
355
G335
6Q3
357
Y335
8L3
359
L336
0
D336
3�
V336
6H3
367
F336
8I3
369
K337
0I3
371
A337
2R3
373
F337
4L3
375
P337
6T3
377
V338
1
S338
7Y3
388
R338
9R3
390
L339
1M3
392
I339
3R3
394
G339
5
G339
8S3
399
V340
0H3
401
S340
2F3
403
A340
4V3
405
Q340
6Y3
407
P340
8A3
409
V341
0R3
411
R341
5E3
416
E341
7R3
418
Q342
1L3
422
Page 6 Full wwPDB EM Validation Report EMD-6816, 5Y81
Y342
3R3
424
L342
5F3
426
N342
7K3
428
K343
2N3
433
V343
4E3
435
T343
6R3
437
R343
8R3
439
S344
0I3
441
Q344
2F3
443
N344
4L3
445
P344
6I3
447
A344
8I3
449
P345
0L3
451
S345
2P3
453
Q345
4V3
455�
R345
6I3
457
M345
8
S346
1V3
462
S346
3F3
464
T346
5T3
466
L346
7H3
468
N347
2E3
473
F347
4
G347
9F3
480
D348
1P3
482
D348
3D3
484
I348
5Q3
486
D348
7F3
488
M348
9A3
490
D349
1K3
492
L349
3N3
494
A349
5A3
496
H349
7D3
498
D349
9AL
ALE
UPR
OA3
503
P350
4D3
505
M350
6T3
507
I350
8L3
509
K351
0V3
511
E351
2I3
513
F351
4N3
515
S351
6I3
517
Q351
8T3
519
M352
0F3
521
V352
2PR
OSE
RN3
525
V352
6L3
527
K352
8D3
529
H353
0F3
531
F353
5TH
RGL
NF3
538
E353
9D3
540
F354
1W3
542
L354
3F3
544
R354
5K3
546
Q354
7
S355
0Q3
551
Y355
2S3
553
S355
4F3
555
V355
6F3
557
M355
8S3
559
Y356
0
T356
8P3
569
H357
0K3
571
I357
2H3
573
V357
4D3
575
K357
6T3
577�
S357
8G3
579
N358
0V3
581
F358
2T3
583
M358
6L3
587
R359
0F3
591�
P359
2�
R359
5
P359
8L3
599
N360
2
L360
5SE
RLE
UPR
OPR
OD3
610�
S361
1P3
612
N361
7E3
618
P361
9V3
620
T362
5P3
626
N362
7
I363
2G3
633
N364
4L3
645
F364
6T3
647
I364
8S3
649
R365
0A3
651
L365
2I3
653
E365
4P3
655
D365
6N3
657
E365
8L3
659
N366
0T3
661
Y366
2L3
663
A366
4L3
665�
F366
6I3
667
R366
8D3
669
E367
0I3
671
I367
2S3
673
W367
4
L367
8H3
679
R368
0PR
OIL
EIL
EGL
UAS
NPR
OQ3
687
V369
2
V369
6D3
697
L369
8I3
699
I370
0R3
701
K370
2V3
703
A370
4Q3
705
L370
6G3
707
H370
8�
L370
9
T371
2P3
713
T371
4V3
715
T371
6T3
717
Q371
8F3
719
I372
0L3
721
D372
2C3
723
I372
4
A372
7
R373
1N3
732
L373
3
D373
7V3
738
N373
9F3
740
M374
1P3
742
W374
3F3
744
• Molecule 2: Chromatin modification-related protein EAF1
Chain C:
PRO
T648
I649
S652
E653
N663
�
E670
S673
A674
H675
M676
T677
H678
R679
L680
T681
Y684
L685
S686
N687
I688
E689
R690
R691
T692
P693
W694
Q695
C696
F697
E698
R699
F700
V701
Q702
L703
N704
E705
R706
F707
D711
L712
�K7
13G7
14P7
15R7
16A7
17H7
18S7
19A7
20Q7
21Q7
22W7
23L7
24
I725
E726
Q732
R733
Q734
S739
P740
�
Q749
�
R754
A758
A763
C767
E772
ASN
THR
PRO
ARG
PRO
ASN
PRO
THR
GLN
PRO
ARG
LYS
PRO
LEU
ASP
CYS
LYS
ASN
MET
LYS
VAL
PRO
T795
P796
A797
L801
Q805
A809
LEU
ARG
ARG
ASP
ILE
GLN
LEU
ARG
ARG
THR
VAL
LYS
ASN
ARG
LEU
GLN
GLN
ARG
GLN
GLN
GLN
SER
GLN
GLN
ALA
HIS
SER
SER
ARG
ALA
GLN
SER
PRO
ILE
PRO
SER
ASN
GLY
LYS
SER
SER
SER
ASN
LEU
ALA
ARG
ASN
GLY
GLN
ALA
SER
ALA
PRO
ARG
PRO
ASN
GLN
LYS
GLN
TYR
THR
GLU
GLN
ASP
ILE
ILE
GLU
SER
TYR
SER
ARG
LYS
LEU
LEU
GLU
GLN
LYS
PRO
ASP
ILE
GLY
PRO
GLU
MET
ALA
LEU
LYS
ALA
ALA
LYS
ASN
TYR
TYR
ARG
THR
LEU
ARG
GLU
GLN
GLN
GLN
GLN
LEU
LYS
GLN
HIS
GLN
ILE
GLN
GLN
GLN
ARG
GLN
GLN
LEU
GLN
GLU
GLU
SER
SER
HIS
VAL
GLN
GLN
LEU
GLN
GLN
LEU
GLN
PRO
GLY
SER
GLN
ALA
PRO
PRO
PRO
LYS
SER
SER
PRO
SER
GLN
SER
SER
LEU
SER
ASN
ILE
SER
ASN
ILE
ASN
SER
ALA
PRO
ARG
ILE
LYS
SER
PRO
THR
PRO
GLN
GLU
ILE
LEU
GLN
ARG
PHE
GLN
LYS
GLN
• Molecule 3: Eaf1-disorder domain
Chain D:
X1 X2 X3 X4 X7 X8 X11
X12
X13
�
X16
X30
�
X38
X39
X55
X59
X60
X61
X62
X63
X64
X65
X66
X74
X75
X79
X80
X81
X82
�X8
3�
X87
�X8
8�
X102
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
X139
X140
X145
�X1
46�
X150
X151
X152
X153
X154
X155
X156
X159
X160
X161
X162
X165
X166
X167
�X1
68X1
69X1
70X1
71X1
72X1
73X1
74X1
75X1
76�
X180
X181
�X1
82
X185
X186
�
X215
X216
X233
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
X266
X277
X278
X281
X282
X285
X286
X289
X290
X306
UNK
UNK
X309
X310
X313
X328
X331
UNK
Page 7 Full wwPDB EM Validation Report EMD-6816, 5Y81
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
X362
X373
X381
�
X384
X385
X386
X396
X397
�
X403
�
X414
X415
X416
X417
X418
X419
X420
X421
X422
X423
X424
X425
X426
X427
X428
X429
X430
X438
�X4
39X4
40X4
41X4
42X4
43X4
44
X458
�X4
59X4
60�
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
UNK
• Molecule 4: Chromatin modification-related protein EAF5
Chain H:
MET
ASP
K3 Q12
T16
S19
�AS
NLY
SAS
NGL
UE2
4L2
5
N28
G29
G30
G31
ILE
ASN
MET
ILE
GLY
ASN
ASN
LEU
ARG
ILE
SER
LEU
VAL
K45
Q51
L54
L55
I56
N57
E58
L59
T60
N61
L62
R63
�AR
GGL
NSE
RAS
NVA
LAL
AAS
NGL
YAS
NAR
GLY
SLE
UG7
6
N86
P89
T93
THR
LEU
ASN
ASP
GLY
GLN
LEU
SER
LEU
HIS
GLY
LEU
E106
M107
�H1
08D1
09
L113
L114
D115
E116
K117
Y118
D119
K122
I129
R130
M131
E135
ILE
LEU
LYS
ASN
GLY
ILE
K142
Q147
LEU
GLN
PRO
HIS
ALA
ASN
ALA
GLY
LYS
SER
GLY
SER
ALA
GLY
THR
SER
ALA
THR
ILE
THR
THR
THR
THR
PRO
HIS
MET
ALA
HIS
SER
MET
ASP
PRO
LYS
R181
�E1
82K1
83L1
84L1
85K1
86L1
87Y1
88R1
89D1
90T1
91V1
92L1
93N1
94K1
95L1
96
T200
GLY
ASN
PHE
GLN
LYS
LEU
PHE
LYS
SER
PRO
ASP
GLY
SER
ILE
ILE
LYS
ASN
GLU
ILE
ASN
TYR
E222
D223
E227
T228
P229
G230
S231
L235
I243
THR
ASP
GLY
VAL
MET
ARG
LYS
VAL
ILE
GLY
THR
ASP
D256
�
R261
F265
D269
THR
VAL
GLN
PHE
MET
ARG
ARG
ALA
LEU
GLU
• Molecule 5: Transcription-associated protein 1
Chain A:
MET
SER
LEU
T4 F14
ARG
ASP
ASP
ASP
ALA
THR
L21
Y25
L31
M35
E36
LEU
LEU
ASN
SER
P41
L56
ASN
GLN
LEU
LYS
GLU
VAL
PRO
ILE
SER
TYR
ASP
ALA
HIS
S70
�
K74
�
R85
CYS
LEU
MET
ASN
GLN
T91
S105
�V1
06�
LEU
PRO
LYS
GLU
N111
M119
L122
T123
K130
SER
ILE
LEU
GLN
ASP
K136
L137
D138
S139
F140
F159
TYR
GLU
ALA
GLY
LYS
ALA
GLU
GLN
GLY
ASP
LEU
ASP
SER
PRO
LYS
GLU
PRO
GLN
ALA
ASP
GLU
LEU
LEU
ASP
GLU
PHE
SER
LYS
ASN
ASP
GLU
GLU
LYS
ASP
PHE
PRO
SER
LYS
GLN
SER
SER
THR
GLU
PRO
ARG
PHE
GLU
ASN
SER
THR
SER
SER
ASN
GLY
L214
S217
M218
F219
S220
C227
PRO
ILE
T230
M231
Y235
�
K239
Q240
L241
T242
S243
T244
S245
L246
L256
LEU
ASN
ILE
GLN
ILE
LYS
GLN
GLN
GLN
GLU
ALA
ARG
GLU
GLN
ALA
GLU
SER
ARG
GLY
GLU
HIS
PHE
THR
SER
ILE
SER
THR
GLU
ILE
ILE
N287
�R2
88P2
89�
T302
S303
F304
L305
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P315
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PHE
LEU
GLN
D320
L328
I329
I330
R331
L332
L333
Q334
D335
C336
PRO
SER
GLU
L340
S341
K345
E346
L347
L348
H349
A350
T351
R352
H353
T357
L362
PHE
LEU
PRO
LYS
L367
D368
Y369
D372
E373
L376
G380
PHE
THR
MET
H384
P389
L390
A391
Y392
E405
LEU
GLN
LEU
SER
E410
I411
E412
D424
E425
S426
T430
V431
Q432
I433
K451
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UAS
NPR
OGL
NGL
UAL
AP4
58
K461
M465
R474
L478
D483
M486
K487
G490
R491
L503
�
LYS
ASN
SER
ILE
GLN
D509
N510
D511
K512
E513
�S5
14E5
15E5
16F5
17M5
18R5
19
L522
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OSE
RAS
PAS
PAS
PHI
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OAS
PVA
LGL
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TTH
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USE
RAS
PLY
SVA
LVA
LLY
SAS
NAS
PVA
LE5
59
Y566
A567
P568
Page 8 Full wwPDB EM Validation Report EMD-6816, 5Y81
L572
P573
T574
P575
D578
P579
I580
K581
D582
A583
Y587
R588
M591
S592
F593
L594
K595
T596
I597
L601
F604
N605
PRO
PRO
PRO
ASN
GLU
TYR
THR
VAL
ALA
ASN
PRO
LYS
LEU
TRP
ALA
SER
VAL
SER
ARG
VAL
PHE
SER
TYR
E629
E630
V631
F634
K635
D636
L637
F638
F648
LYS
ASP
HIS
ASN
GLU
LYS
LEU
SER
PRO
GLU
THR
THR
LYS
LYS
HIS
PHE
ASP
ILE
SER
MET
PRO
SER
LEU
PRO
VAL
S674
E681
L682
Y685
L686
F690
M691
Q692
MET
ASP
ASN
A696
P707
F708
V709
M713
L714
GLU
ASP
SER
G718
T732
SER
PRO
ASN
F736
L741
L744
L751
GLY
ASN
VAL
ASP
PHE
N757
F776
P777
P786
H787
L791
S799
THR
THR
ALA
GLU
E804
P805
L806
F809
T814
S818
P833
I834
L838
L842
M845
ILE
LEU
THR
ALA
ARG
L851
P852
E856
E860
P866
V871
L872
A873
P874
Y875
L876
P877
F878
K881
P882
Q889
Y890
P891
D892
L893
V894
G897
T900
L901
Y912
F913
D914
P915
I916
I917
V924
A927
N930
LEU
LEU
GLN
PRO
GLN
PRO
PHE
N938
I948
L952
�G9
53
R957
Q958
F959
L960
K961
P962
P963
T964
D965
L966
T967
E968
K969
T970
E971
L972
D973
A976
�I9
77A9
78D9
79F9
80K9
81I9
82N9
83
P986
E987
D988
V989
P990
L991
S992
V993
T994
P995
G996
I997
Q998
I100
3
S100
6
S100
9D1
010
I101
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012
Y101
3R1
014
K101
5S1
016�
A101
7
L102
7
K103
0S1
031
S103
2A1
033
E103
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035
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6T1
037
N103
8Y1
039
T104
0E1
041
L104
2L1
043
K104
4T1
045
A104
6
K105
1
V106
7N1
068
K106
9R1
070
D107
1Y1
072
V108
6
T109
0S1
091
I109
2K1
093
E109
4L1
095
K109
6D1
097
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8A1
099
M110
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101�
L110
2L1
103
N110
4N1
105
L110
6L1
107
C111
1
T111
7
N112
1
N112
6GL
YTH
RPH
EAS
NIL
EAS
PLE
ULY
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NPH
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TLE
UAS
PS1
142�
S114
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144�
A114
8�
A115
2
L115
3S1
154
I115
7P1
158
E115
9
K117
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RCY
SLE
UIL
ETY
RGL
YGL
UE1
182
L120
0C1
201
Y120
2D1
203�
E120
4
Y120
7N1
208
K120
9R1
210
N122
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223
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225
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230
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248
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251
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256
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258
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2
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5
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PVA
LLY
S
GLU
GLU
ASP
L128
0�
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6
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295
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6
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301
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2
S131
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NLE
UT1
318
P132
1
S133
5P1
336
ILE
PHE
ALA
LYS
PRO
LEU
ARG
ALA
L134
5P1
346
M134
9
A135
6
L136
1S1
362
L136
3P1
364
E137
2E1
373
L137
4F1
375
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377
A138
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UAS
P
GLU
SER
LEU
SER
THR
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ILE
GLN
LYS
THR
T140
0
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7
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421
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2L1
423
LYS
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GLU
GLU
PHE
ALA
THR
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1
L144
1
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3
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6
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8
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535
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L154
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546
M154
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0
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567
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581
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583
L158
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585
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6Q1
587
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8D1
589
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591
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597
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8
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606
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608
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5
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630
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647
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653
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662
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674
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676
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UTR
PLE
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5
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ASP
A179
8
A181
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N
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VAL
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ASP
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H185
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858
L185
9F1
860
R186
1F1
862
L186
7S1
868
F187
1I1
872
LYS
ALA
ASP
PRO
GLU
ILE
I187
9
I189
4K1
895
L189
6E1
897
D189
8
F191
2IL
ESE
RLY
SPH
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917
F191
8P1
919
R193
2SE
RSE
RHI
SVA
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937
A193
8
V194
2
V194
8
P195
1V1
952
L195
3
HIS
GLU
ARG
MET
ASN
ALA
A196
0G1
961
T196
2P1
963
D196
4T1
965
W196
6I1
967
N196
8
V197
3ME
TVA
LGL
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979
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F198
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989
I199
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H199
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993
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UPH
EPH
EN1
998
S200
5
H200
9
N201
2
F201
6M2
017
SER
ASN
SER
ASN
SER
D202
3
L203
6Y2
037
W203
8E2
039
L204
3GL
U
Page 9 Full wwPDB EM Validation Report EMD-6816, 5Y81
ILE
THR
ASN
VAL
ASN
ASN
THR
LYS
THR
ASP
SER
ASP
GLY
ASP
VAL
VAL
MET
SER
ASP
SER
LYS
SER
ASP
ILE
ASN
PRO
VAL
GLU
ALA
ASP
THR
THR
ALA
ILE
ILE
VAL
ASP
ALA
ASN
ASN
ASN
SER
PRO
ILE
SER
L209
0H2
091
L209
2
A209
5
S210
7AS
NHI
SAR
GAL
AIL
EGL
UTH
RE2
115
D213
0LY
SHI
STR
PTH
RAS
NVA
LAS
NVA
LLY
SL2
140
L214
7IL
EPH
EGL
NAS
PLE
UAS
PSE
RE2
155
L216
8Y2
169
F217
2K2
173
N217
4�
W217
9I2
180
M218
1E2
182
N218
3L2
184
P218
5
I219
5LY
SSE
RAS
PHI
SHI
SAS
PV2
202
A221
9GL
NGL
YVA
LSE
RVA
LI2
225
I222
6
E222
9
I224
3T2
244
GLN
ASP
LEU
GLN
GLU
THR
S225
1S2
252
V225
3
G225
6V2
257
A226
0W2
261
F226
7PR
OAS
PN2
270
H228
9LE
USE
RIL
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RGL
NPR
OLY
SAS
PAL
AME
TAL
AL2
301
L231
8SE
RLE
ULY
SVA
LSE
RLE
UL2
325
P233
1
S233
4
L233
8
I235
2
S235
6
I236
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EAS
NTH
RGL
UIL
E
PHE
P236
7T2
368
V236
9K2
370
A238
1
I238
4
S238
9L2
390
S239
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392
L240
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402
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408�
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410
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415
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420
L242
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430
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ELY
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450
W246
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7
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USE
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SN2
490
I249
1
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5E2
506
V251
1
V251
4
L251
7E2
518
L251
9
K252
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H252
6I2
527
A252
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529
M253
0
L253
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GIL
EIL
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538
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9
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1
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4
L260
7
K261
2
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A
• Molecule 6: Actin-related protein 4
Chain F:
P0 M1 S2 L6 Q7 V8 Y9�
G10
G11
D12
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A16
V17
V18
I19
D20
P21
G22
S23
Y24
T25
T26
N27
I28
G29
Y30
S31
G32
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F35
P36
L40
P41
S42
V43
Y44
G45
K46
Y47
T48
A49
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3
I56
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7S5
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S61
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P65
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6K6
7D6
8Y6
9
E70
L71
K72
P73
I74
V80
I81
D82
W83
D84
T85
A86
Q87
E88
Q89
W90
Q91
W92
A93
L94
Q95
N96
E97
L98
Y99
L100
G105
I106
P107
L110
T111
E112
P113
V114
W115
N116
S117
T118
E119
N120
R121
K122
K123
S124
L125
E126
V127
L128
L129
M132
Q133
F134
E135
�A1
36C1
37
C145
F148
G151
R152
P153
L156
D163
T164
S168
P169
I170
V171
M174
T175
L176
S177
K178
S179
T180
R181
R182
N183
F184
I185
A186
G187
K188
F189
I190
N191
H192
L193
I194
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I204
P205
K210
Q211
R212
K213
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14E2
15F2
16I2
17K2
18K2
19T2
20�
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D226
L229
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A233
N234
G237
F238
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C242
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E244
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L246
C247
H248
I249
K253
T254
L255
E256
E257
T258
E261
S264
T265
A266
K267
S272
P273
W274
N275
E276
E277
�I2
78
N282
R285
Y286
G287
F288
A289
E290
E291
L292
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E297
D298
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99I3
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01
A302
N303
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04P3
05R3
06S3
07N3
08S3
09G3
10V3
11VA
LLY
STH
RTR
PAR
GAS
NAS
PTY
RVA
LPR
OLE
ULY
SAR
GTH
RLY
SPR
OSE
RGL
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LAS
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RAS
PLY
SLY
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RGL
UGL
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SGL
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NGL
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AVA
LSE
RLY
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RTH
RSE
RPR
OAL
AAL
AAS
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RAL
AAS
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R
PRO
ASN
GLU
THR
GLY
LYS
ARG
PRO
LEU
GLU
GLU
GLU
LYS
PRO
PRO
LYS
GLU
ASN
ASN
E381
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L388
V389
Y390
D397
L400
R401
L404
A405
H406
N407
G412
G413
T414
S415
S416
L420
L428
L432
P433
S434
L435
K436
F437
R438
I439
L440
T441
T442
G443
H444
Page 10 Full wwPDB EM Validation Report EMD-6816, 5Y81
T445
I446
E447
R448
Q449
Y450
Q451
S452
W453
L454
G455
I458
L459
T460
S461
L462
G463
T464
F465
H466
Q467
L468
W469
Y475
L483
L484
R487
�F4
88�
R489
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• Molecule 7: Actin
Chain G:
MET
ASP
SER
GLU
V5 A6�
A7 L8 V9 I10
S14
G15
M16
C17
K18
A19
G20
F21
A22
G23
�D2
4�
D25
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Page 11 Full wwPDB EM Validation Report EMD-6816, 5Y81
4 Experimental information i○
Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, Not providedNumber of particles used 63197 DepositorResolution determination method FSC 0.143 CUT-OFF DepositorCTF correction method PHASE FLIPPING AND AMPLITUDE
CORRECTIONDepositor
Microscope FEI TITAN KRIOS DepositorVoltage (kV) 300 DepositorElectron dose (e−/Å2
) 30 DepositorMinimum defocus (nm) Not providedMaximum defocus (nm) Not providedMagnification Not providedImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 0.132 DepositorMinimum map value -0.063 DepositorAverage map value 0.000 DepositorMap value standard deviation 0.005 DepositorRecommended contour level 0.0225 DepositorMap size (Å) 374.4, 374.4, 374.4 wwPDBMap dimensions 288, 288, 288 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.3, 1.3, 1.3 Depositor
Page 12 Full wwPDB EM Validation Report EMD-6816, 5Y81
5 Model quality i○
5.1 Standard geometry i○
The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).
Mol Chain Bond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >5
1 B 0.36 0/5992 0.58 2/8237 (0.0%)2 C 0.29 0/805 0.57 2/1110 (0.2%)4 H 0.31 0/755 0.48 2/1039 (0.2%)5 A 0.28 1/9944 (0.0%) 0.51 32/13772 (0.2%)6 F 0.39 0/3406 0.56 0/46187 G 0.40 0/2787 0.54 0/37768 E 0.43 0/351 0.60 0/473All All 0.34 1/24040 (0.0%) 0.54 38/33025 (0.1%)
All (1) bond length outliers are listed below:
Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)5 A 410 GLU C-N 9.50 1.55 1.34
All (38) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 A 777 PRO N-CA-CB 6.52 111.12 103.301 B 3129 PRO N-CA-CB 6.48 111.08 103.305 A 891 PRO N-CA-CB 6.46 111.05 103.305 A 1919 PRO N-CA-CB 6.36 110.93 103.304 H 89 PRO N-CA-CB 6.30 110.86 103.305 A 707 PRO N-CA-CB 6.24 110.78 103.305 A 2497 PRO N-CA-CB 6.21 110.75 103.305 A 786 PRO N-CA-CB 6.19 110.72 103.305 A 573 PRO N-CA-CB 6.16 110.69 103.305 A 1474 PRO N-CA-CB 6.13 110.66 103.305 A 575 PRO N-CA-CB 6.00 110.49 103.305 A 579 PRO N-CA-CB 5.94 110.43 103.305 A 2331 PRO N-CA-CB 5.87 110.34 103.302 C 796 PRO N-CA-CB 5.86 110.33 103.305 A 1336 PRO N-CA-CB 5.85 110.32 103.305 A 1963 PRO N-CA-CB 5.83 110.29 103.30
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Page 13 Full wwPDB EM Validation Report EMD-6816, 5Y81
Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 A 882 PRO N-CA-CB 5.80 110.26 103.305 A 833 PRO N-CA-CB 5.77 110.23 103.305 A 2496 PRO N-CA-CB 5.77 110.22 103.302 C 740 PRO N-CA-CB 5.74 110.19 103.305 A 1993 PRO N-CA-CB 5.74 110.18 103.305 A 1951 PRO N-CA-CB 5.73 110.18 103.305 A 1548 PRO N-CA-CB 5.69 110.12 103.301 B 2921 PRO N-CA-CB 5.68 110.11 103.305 A 877 PRO N-CA-CB 5.67 110.10 103.305 A 2185 PRO N-CA-CB 5.63 110.05 103.305 A 458 PRO N-CA-CB 5.61 110.03 103.305 A 874 PRO N-CA-CB 5.61 110.03 103.305 A 1563 PRO N-CA-CB 5.60 110.02 103.305 A 1321 PRO N-CA-CB 5.55 109.96 103.305 A 1453 PRO N-CA-CB 5.52 109.92 103.305 A 852 PRO N-CA-CB 5.50 109.90 103.305 A 805 PRO N-CA-CB 5.49 109.88 103.305 A 1742 PRO N-CA-CB 5.49 109.88 103.304 H 229 PRO N-CA-CB 5.46 109.84 103.305 A 866 PRO N-CA-CB 5.27 109.63 103.305 A 568 PRO N-CA-CB 5.16 109.49 103.305 A 2505 PRO N-CA-CB 5.15 109.48 103.30
There are no chirality outliers.
There are no planarity outliers.
5.2 Too-close contacts i○
In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashes withinthe asymmetric unit, whereas Symm-Clashes lists symmetry-related clashes.
Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 B 5937 0 4061 713 02 C 800 0 481 63 03 D 1800 0 405 60 04 H 764 0 309 24 05 A 10017 0 4245 320 06 F 3334 0 3292 264 07 G 2729 0 2697 238 0
Continued on next page...
Page 14 Full wwPDB EM Validation Report EMD-6816, 5Y81
Continued from previous page...Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes8 E 342 0 331 40 0All All 25723 0 15821 1656 0
The all-atom clashscore is defined as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 40.
All (1656) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3106:TRP:CZ3 1:B:3668:ARG:HD2 1.26 1.697:G:163:VAL:CG2 7:G:175:ILE:HG12 1.24 1.677:G:163:VAL:HG22 7:G:175:ILE:CG1 1.28 1.647:G:163:VAL:CG2 7:G:175:ILE:CG1 1.76 1.591:B:3139:GLN:CB 1:B:3418:ARG:HH21 1.07 1.587:G:163:VAL:CG2 7:G:175:ILE:CD1 1.81 1.571:B:3236:ARG:HG3 1:B:3338:CYS:CB 1.30 1.541:B:3474:PHE:CE2 1:B:3526:VAL:HG21 1.38 1.531:B:3427:ASN:CB 1:B:3443:PHE:HE1 1.17 1.531:B:3106:TRP:CH2 1:B:3668:ARG:HD2 1.39 1.521:B:3171:LEU:HD23 1:B:3172:ARG:N 1.22 1.521:B:3474:PHE:CE2 1:B:3526:VAL:CG2 1.90 1.515:A:2243:ILE:HA 5:A:2252:SER:CB 1.39 1.511:B:3427:ASN:HB2 1:B:3443:PHE:CE1 1.47 1.491:B:3625:THR:CB 1:B:3727:ALA:HB1 1.39 1.481:B:3403:PHE:CB 1:B:3457:ILE:HB 1.42 1.471:B:3043:PHE:CB 1:B:3060:TRP:NE1 1.77 1.471:B:3106:TRP:CH2 1:B:3668:ARG:CD 1.98 1.471:B:3106:TRP:HH2 1:B:3668:ARG:CG 1.24 1.461:B:3731:ARG:NH2 2:C:694:TRP:CD1 1.82 1.461:B:2828:TRP:CB 1:B:2842:LEU:HD21 1.45 1.451:B:2828:TRP:CB 1:B:2842:LEU:CD2 1.97 1.421:B:3427:ASN:CB 1:B:3443:PHE:CE1 2.01 1.411:B:3139:GLN:CB 1:B:3418:ARG:NH2 1.83 1.391:B:3043:PHE:CB 1:B:3060:TRP:HE1 1.33 1.381:B:2633:TRP:CB 5:A:2624:LYS:CB 1.99 1.381:B:3731:ARG:NH2 2:C:694:TRP:HD1 1.08 1.381:B:3253:LEU:CD2 1:B:3314:LEU:CB 2.00 1.371:B:3731:ARG:HD2 2:C:694:TRP:NE1 1.39 1.342:C:721:GLN:O 2:C:724:LEU:CB 1.75 1.34
1:B:3244:ASP:HA 1:B:3247:ARG:CD 1.57 1.331:B:3367:HIS:HE1 5:A:912:TYR:O 1.08 1.32
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Page 15 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3568:THR:HB 1:B:3569:PRO:CD 1.56 1.321:B:3705:GLN:CB 1:B:3709:LEU:HA 1.61 1.311:B:3106:TRP:CH2 1:B:3668:ARG:CG 2.09 1.301:B:3450:PRO:C 1:B:3451:LEU:HD12 1.49 1.301:B:3427:ASN:CA 1:B:3443:PHE:CE1 2.11 1.301:B:3667:ILE:CD1 1:B:3692:VAL:CB 2.12 1.286:F:442:THR:CG2 6:F:448:ARG:HE 1.45 1.271:B:3424:ARG:NH1 1:B:3447:ILE:HA 1.50 1.261:B:3719:PHE:HA 1:B:3722:ASP:OD2 1.34 1.255:A:333:LEU:CB 5:A:376:LEU:CB 2.14 1.253:D:418:UNK:CB 6:F:441:THR:H 1.50 1.235:A:1093:LYS:O 5:A:1095:LEU:N 1.71 1.225:A:430:THR:O 5:A:432:GLN:N 1.73 1.211:B:3427:ASN:CA 1:B:3443:PHE:HE1 1.45 1.211:B:3374:PHE:CB 1:B:3392:MET:CB 2.17 1.21
1:B:3100:LEU:HD13 1:B:3101:LEU:N 1.56 1.216:F:444:HIS:O 6:F:446:ILE:N 1.70 1.21
7:G:163:VAL:HG21 7:G:175:ILE:CD1 1.50 1.201:B:3474:PHE:CD2 1:B:3526:VAL:HG11 1.74 1.201:B:3163:TYR:CB 1:B:3167:LEU:CD2 2.21 1.195:A:1372:GLU:O 5:A:1375:PHE:N 1.76 1.185:A:1043:LEU:O 5:A:1046:ALA:HB3 1.43 1.181:B:3450:PRO:O 1:B:3451:LEU:CD1 1.91 1.176:F:213:LYS:HB3 6:F:214:PRO:CD 1.70 1.175:A:2243:ILE:CB 5:A:2252:SER:C 2.14 1.171:B:3568:THR:HB 1:B:3569:PRO:HD2 1.18 1.175:A:1363:LEU:O 5:A:1364:PRO:CB 1.85 1.16
1:B:3474:PHE:CE2 1:B:3526:VAL:HG22 1.76 1.166:F:62:ILE:O 6:F:71:LEU:HD21 1.45 1.16
1:B:3528:LYS:CB 1:B:3632:ILE:O 1.93 1.161:B:3427:ASN:HA 1:B:3443:PHE:CE1 1.78 1.151:B:3236:ARG:CG 1:B:3338:CYS:CB 2.24 1.155:A:1091:SER:CB 5:A:1099:ALA:HA 1.76 1.151:B:3360:LEU:CB 1:B:3424:ARG:HH21 1.57 1.141:B:3099:GLU:HB2 1:B:3425:LEU:HD11 1.16 1.141:B:3106:TRP:CH2 1:B:3668:ARG:CB 2.29 1.141:B:3496:ALA:HB1 2:C:684:TYR:CE1 1.83 1.141:B:3106:TRP:HH2 1:B:3668:ARG:CD 1.43 1.141:B:3367:HIS:CE1 5:A:912:TYR:O 1.99 1.145:A:1091:SER:CA 5:A:1099:ALA:HB2 1.77 1.131:B:3450:PRO:O 1:B:3451:LEU:HD12 0.95 1.13
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Page 16 Full wwPDB EM Validation Report EMD-6816, 5Y81
Continued from previous page...
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3068:LEU:HD23 1:B:3081:ALA:CB 1.76 1.135:A:2243:ILE:CA 5:A:2252:SER:CB 2.26 1.121:B:3625:THR:CB 1:B:3727:ALA:CB 2.26 1.125:A:631:VAL:CB 5:A:1587:GLN:CB 2.26 1.125:A:137:LEU:O 5:A:139:SER:N 1.82 1.121:B:2690:ILE:HA 1:B:3715:VAL:CB 1.80 1.116:F:213:LYS:HB3 6:F:214:PRO:HD2 1.24 1.111:B:3360:LEU:CB 1:B:3424:ARG:NH2 2.13 1.111:B:2647:THR:CB 1:B:2651:ASN:OD1 1.99 1.101:B:2659:GLU:HG3 1:B:2681:ARG:CB 1.80 1.101:B:3740:PHE:C 1:B:3742:PRO:HD3 1.68 1.10
1:B:3171:LEU:CD2 1:B:3172:ARG:N 2.12 1.101:B:3244:ASP:HA 1:B:3247:ARG:HD3 1.17 1.101:B:3106:TRP:HB2 1:B:3665:LEU:HD13 1.16 1.105:A:239:LYS:O 5:A:241:LEU:N 1.83 1.09
1:B:3253:LEU:HD21 1:B:3314:LEU:CB 1.76 1.091:B:3053:LEU:CB 1:B:3056:ALA:HB2 1.82 1.091:B:3496:ALA:HB1 2:C:684:TYR:HE1 0.98 1.091:B:3106:TRP:CZ3 1:B:3668:ARG:CD 2.21 1.09
6:F:87:GLN:O 6:F:132:MET:HE3 1.49 1.081:B:3427:ASN:HA 1:B:3443:PHE:CZ 1.87 1.086:F:442:THR:HG21 6:F:448:ARG:HE 1.07 1.081:B:3116:MET:O 1:B:3119:ASN:N 1.86 1.081:B:3568:THR:CB 1:B:3569:PRO:CD 2.28 1.085:A:1292:ILE:O 5:A:1294:CYS:N 1.86 1.087:G:138:ALA:CB 7:G:165:ILE:HD11 1.83 1.087:G:163:VAL:HG22 7:G:175:ILE:CD1 1.58 1.071:B:3407:TYR:H 1:B:3408:PRO:CD 1.69 1.065:A:1091:SER:CB 5:A:1099:ALA:CB 2.33 1.061:B:3068:LEU:HB2 1:B:3078:ALA:CB 1.86 1.061:B:3106:TRP:HH2 1:B:3668:ARG:HG3 1.17 1.061:B:3163:TYR:CB 1:B:3167:LEU:HD23 1.82 1.062:C:673:SER:HA 2:C:681:THR:HG21 1.36 1.06
7:G:163:VAL:HG21 7:G:175:ILE:HD13 1.08 1.061:B:2828:TRP:CB 1:B:2842:LEU:HD23 1.78 1.051:B:3068:LEU:HD23 1:B:3081:ALA:HB3 1.33 1.051:B:2638:ASN:O 1:B:2642:SER:N 1.89 1.05
1:B:3474:PHE:CD2 1:B:3526:VAL:HG21 1.91 1.051:B:3068:LEU:HB2 1:B:3078:ALA:HB1 1.33 1.051:B:3705:GLN:CB 1:B:3709:LEU:CA 2.33 1.051:B:2670:GLN:CA 1:B:2837:PRO:HG3 1.85 1.05
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Page 17 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3450:PRO:C 1:B:3451:LEU:CD1 2.24 1.051:B:3163:TYR:CB 1:B:3167:LEU:HD22 1.86 1.055:A:1859:LEU:O 5:A:1861:ARG:N 1.89 1.05
1:B:3068:LEU:CD2 1:B:3081:ALA:HB3 1.86 1.057:G:163:VAL:HG23 7:G:175:ILE:HG12 1.11 1.051:B:3377:THR:CB 1:B:3390:ARG:O 2.05 1.045:A:1091:SER:HA 5:A:1099:ALA:HB2 1.37 1.041:B:3407:TYR:H 1:B:3408:PRO:HD2 1.22 1.041:B:3043:PHE:CB 1:B:3060:TRP:CD1 2.40 1.035:A:1097:ASP:O 5:A:1099:ALA:N 1.91 1.031:B:3618:GLU:O 1:B:3620:VAL:N 1.90 1.035:A:1152:ALA:O 5:A:1154:SER:N 1.91 1.031:B:3244:ASP:HA 1:B:3247:ARG:HD2 1.37 1.035:A:2243:ILE:CB 5:A:2253:VAL:N 2.19 1.031:B:3403:PHE:CB 1:B:3457:ILE:CB 2.36 1.025:A:424:ASP:O 5:A:426:SER:N 1.91 1.021:B:3719:PHE:O 1:B:3722:ASP:HB2 1.58 1.021:B:3404:ALA:H 1:B:3457:ILE:HG22 1.22 1.025:A:1441:LEU:O 5:A:1445:PHE:N 1.93 1.011:B:3171:LEU:O 1:B:3174:THR:N 1.93 1.01
7:G:163:VAL:HG23 7:G:175:ILE:CG1 1.69 1.013:D:79:UNK:O 3:D:80:UNK:O 1.77 1.01
7:G:163:VAL:CG2 7:G:175:ILE:HD11 1.87 1.011:B:3427:ASN:HB2 1:B:3443:PHE:CD1 1.95 1.015:A:1091:SER:CB 5:A:1099:ALA:CA 2.39 1.001:B:2670:GLN:N 1:B:2837:PRO:HG3 1.76 1.001:B:2638:ASN:O 1:B:2642:SER:HB3 1.62 1.005:A:1043:LEU:O 5:A:1046:ALA:CB 2.10 0.991:B:3618:GLU:O 1:B:3619:PRO:C 1.96 0.992:C:715:PRO:O 2:C:717:ALA:N 1.96 0.99
1:B:3099:GLU:CB 1:B:3425:LEU:HD11 1.91 0.992:C:713:LYS:O 2:C:714:GLY:O 1.79 0.991:B:3703:VAL:O 1:B:3704:ALA:O 1.80 0.991:B:3427:ASN:CA 1:B:3443:PHE:CZ 2.45 0.996:F:87:GLN:O 6:F:132:MET:CE 2.11 0.98
1:B:3474:PHE:CD2 1:B:3526:VAL:CG1 2.46 0.981:B:3649:SER:OG 1:B:3705:GLN:HA 1.63 0.986:F:442:THR:HG21 6:F:448:ARG:NE 1.77 0.985:A:1292:ILE:C 5:A:1294:CYS:H 1.68 0.98
1:B:3244:ASP:CA 1:B:3247:ARG:HD3 1.93 0.971:B:3424:ARG:HH12 1:B:3447:ILE:HA 1.07 0.97
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Page 18 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3741:MET:N 1:B:3742:PRO:CD 2.26 0.971:B:3106:TRP:HB2 1:B:3665:LEU:CD1 1.93 0.976:F:71:LEU:HD11 6:F:229:LEU:HD13 1.45 0.976:F:66:ARG:NH1 6:F:66:ARG:HB3 1.79 0.975:A:1372:GLU:O 5:A:1374:LEU:N 1.97 0.975:A:1157:ILE:O 5:A:1159:GLU:N 1.95 0.97
1:B:2659:GLU:CG 1:B:2681:ARG:CB 2.42 0.975:A:1227:SER:O 5:A:1231:LYS:CB 2.12 0.961:B:3411:ARG:O 1:B:3415:ARG:N 1.97 0.966:F:91:GLN:HB2 6:F:132:MET:CE 1.95 0.965:A:1300:ASN:O 5:A:1302:LYS:N 1.98 0.966:F:211:GLN:OE1 6:F:217:ILE:HD12 1.65 0.961:B:3085:TYR:C 1:B:3104:ILE:CD1 2.34 0.961:B:3391:LEU:O 1:B:3402:SER:CB 2.14 0.953:D:418:UNK:CB 6:F:441:THR:N 2.28 0.951:B:3424:ARG:NE 1:B:3445:LEU:CB 2.29 0.951:B:3649:SER:CB 1:B:3705:GLN:HA 1.96 0.951:B:3492:LYS:HE3 1:B:3492:LYS:HA 1.48 0.955:A:516:GLU:O 5:A:518:MET:N 2.00 0.941:B:3422:LEU:H 1:B:3422:LEU:HD22 1.27 0.946:F:442:THR:CG2 6:F:448:ARG:NE 2.30 0.941:B:2822:GLN:O 1:B:2825:LEU:N 1.99 0.94
1:B:3253:LEU:HD23 1:B:3314:LEU:CB 1.97 0.941:B:3106:TRP:CH2 1:B:3668:ARG:HB3 1.99 0.941:B:3668:ARG:HE 1:B:3672:ILE:HD13 1.32 0.941:B:3171:LEU:HD23 1:B:3172:ARG:CA 1.98 0.941:B:3247:ARG:HG3 1:B:3247:ARG:HH21 1.33 0.941:B:3171:LEU:CD2 1:B:3172:ARG:H 1.76 0.941:B:3649:SER:HB2 1:B:3704:ALA:O 1.68 0.931:B:3053:LEU:CB 1:B:3056:ALA:CB 2.45 0.938:E:391:ILE:HA 8:E:394:TYR:HB2 1.48 0.932:C:722:GLN:C 2:C:724:LEU:H 1.72 0.92
7:G:138:ALA:HB1 7:G:165:ILE:HD11 1.47 0.921:B:3740:PHE:CB 1:B:3742:PRO:HD3 1.98 0.926:F:129:LEU:HD22 6:F:129:LEU:H 1.32 0.921:B:2817:CYS:CB 1:B:2852:PHE:CZ 2.52 0.921:B:3474:PHE:CG 1:B:3526:VAL:HG11 2.04 0.921:B:3667:ILE:HD12 1:B:3692:VAL:CB 1.98 0.921:B:3644:ASN:HA 1:B:3647:THR:OG1 1.69 0.926:F:213:LYS:CB 6:F:214:PRO:CD 2.47 0.925:A:244:THR:O 5:A:245:SER:O 1.88 0.92
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Page 19 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3244:ASP:O 1:B:3247:ARG:HG2 1.69 0.921:B:3424:ARG:HE 1:B:3445:LEU:CB 1.83 0.927:G:139:VAL:HG13 7:G:165:ILE:HG21 1.50 0.921:B:2690:ILE:CA 1:B:3715:VAL:CB 2.47 0.911:B:3244:ASP:CA 1:B:3247:ARG:CD 2.46 0.911:B:3667:ILE:HD13 1:B:3692:VAL:CB 1.99 0.917:G:286:ASP:HB3 7:G:288:ASP:OD1 1.71 0.911:B:3731:ARG:CD 2:C:694:TRP:HE1 1.82 0.914:H:51:GLN:O 4:H:55:LEU:N 2.04 0.91
7:G:163:VAL:HG22 7:G:175:ILE:HD11 1.49 0.915:A:1091:SER:CA 5:A:1099:ALA:CB 2.48 0.911:B:3055:LYS:O 1:B:3059:GLN:N 2.03 0.901:B:3740:PHE:C 1:B:3742:PRO:CD 2.39 0.90
1:B:2640:LEU:HD21 1:B:2662:LEU:CB 2.02 0.901:B:3085:TYR:C 1:B:3104:ILE:HD11 1.92 0.901:B:3219:TYR:N 1:B:3220:PRO:HD3 1.87 0.901:B:3731:ARG:CD 2:C:694:TRP:NE1 2.33 0.905:A:1506:LEU:O 5:A:1508:GLU:N 2.04 0.901:B:2638:ASN:O 1:B:2642:SER:CB 2.20 0.90
1:B:3253:LEU:HD22 1:B:3314:LEU:CB 2.00 0.901:B:3618:GLU:CB 1:B:3620:VAL:O 2.20 0.896:F:87:GLN:HG3 6:F:132:MET:HE2 1.54 0.891:B:3106:TRP:HZ3 1:B:3668:ARG:HD2 1.13 0.895:A:1069:LYS:O 5:A:1072:TYR:N 2.05 0.89
1:B:3568:THR:HG22 1:B:3569:PRO:HD3 1.55 0.895:A:511:ASP:O 5:A:515:GLU:CB 2.20 0.89
6:F:442:THR:OG1 6:F:443:GLY:N 2.06 0.891:B:3106:TRP:CH2 1:B:3668:ARG:NH2 2.39 0.881:B:3107:LEU:HA 1:B:3110:ILE:HD12 1.54 0.881:B:3731:ARG:CZ 2:C:694:TRP:HD1 1.85 0.881:B:3407:TYR:N 1:B:3408:PRO:CD 2.34 0.887:G:151:ILE:HG23 7:G:297:ILE:HA 1.54 0.881:B:3568:THR:CB 1:B:3569:PRO:HD3 2.03 0.887:G:151:ILE:HG21 7:G:297:ILE:HG12 1.55 0.885:A:239:LYS:C 5:A:241:LEU:H 1.78 0.87
1:B:2748:GLU:HB3 1:B:2752:HIS:CD2 2.07 0.876:F:428:LEU:HB3 6:F:437:PHE:HE2 1.37 0.871:B:2821:ILE:CB 1:B:2849:TYR:CE2 2.57 0.875:A:511:ASP:O 5:A:515:GLU:N 2.07 0.87
1:B:3474:PHE:CZ 1:B:3526:VAL:HG22 2.09 0.871:B:3354:ILE:HA 1:B:3371:ILE:H 1.39 0.87
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Page 20 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3219:TYR:H 1:B:3220:PRO:HD3 1.38 0.871:B:3418:ARG:O 1:B:3422:LEU:CD2 2.23 0.871:B:3106:TRP:CZ2 1:B:3668:ARG:CB 2.58 0.861:B:3388:TYR:CB 1:B:3404:ALA:HB1 2.04 0.861:B:2961:ASP:C 1:B:2963:CYS:H 1.78 0.861:B:3418:ARG:CB 1:B:3418:ARG:HH11 1.88 0.861:B:3551:GLN:O 1:B:3554:SER:N 2.08 0.866:F:428:LEU:HB3 6:F:437:PHE:CE2 2.09 0.861:B:3474:PHE:HE2 1:B:3526:VAL:CG2 1.52 0.867:G:16:MET:N 7:G:16:MET:SD 2.49 0.865:A:1650:PHE:O 5:A:1652:ILE:N 2.09 0.861:B:3055:LYS:CB 1:B:3059:GLN:HG3 2.06 0.861:B:3652:LEU:O 1:B:3652:LEU:HD22 1.76 0.85
1:B:3169:PHE:CE1 1:B:3451:LEU:HD21 2.09 0.857:G:138:ALA:HA 7:G:152:VAL:HG11 1.56 0.851:B:3526:VAL:O 1:B:3530:HIS:N 2.08 0.856:F:87:GLN:CG 6:F:132:MET:CE 2.54 0.85
1:B:3424:ARG:CD 1:B:3445:LEU:CB 2.53 0.856:F:87:GLN:HG2 6:F:132:MET:HE1 1.56 0.856:F:62:ILE:O 6:F:71:LEU:CD2 2.24 0.85
1:B:2651:ASN:O 1:B:2653:LYS:N 2.09 0.856:F:45:GLY:HA3 6:F:56:ILE:HG22 1.56 0.855:A:1993:PRO:O 5:A:1998:ASN:N 2.10 0.857:G:16:MET:H 7:G:16:MET:CE 1.88 0.85
1:B:3062:PHE:HZ 1:B:3657:ASN:C 1.79 0.857:G:138:ALA:HB3 7:G:165:ILE:HD11 1.58 0.841:B:2821:ILE:HA 1:B:2849:TYR:OH 1.76 0.84
1:B:3731:ARG:HD2 2:C:694:TRP:CD1 2.12 0.841:B:3068:LEU:CB 1:B:3078:ALA:CB 2.55 0.841:B:3703:VAL:O 1:B:3704:ALA:C 2.14 0.841:B:3427:ASN:N 1:B:3443:PHE:CZ 2.45 0.846:F:91:GLN:OE1 6:F:132:MET:SD 2.34 0.841:B:3576:LYS:H 1:B:3576:LYS:HD3 1.43 0.841:B:3618:GLU:O 1:B:3620:VAL:O 1.96 0.845:A:302:THR:O 5:A:304:PHE:N 2.10 0.843:D:155:UNK:O 3:D:159:UNK:N 2.09 0.841:B:3481:ASP:CB 1:B:3482:PRO:CD 2.55 0.845:A:1859:LEU:O 5:A:1862:PHE:N 2.11 0.835:A:914:ASP:O 5:A:915:PRO:C 2.13 0.83
1:B:3568:THR:CG2 1:B:3569:PRO:HD3 2.07 0.831:B:3418:ARG:HB2 1:B:3418:ARG:HH11 1.43 0.83
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Page 21 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3168:HIS:O 1:B:3172:ARG:HB3 1.78 0.836:F:213:LYS:C 6:F:213:LYS:HE3 1.99 0.83
1:B:3168:HIS:HA 1:B:3171:LEU:HD22 1.61 0.831:B:3411:ARG:HD2 1:B:3587:LEU:CB 2.08 0.836:F:91:GLN:HB2 6:F:132:MET:SD 2.19 0.831:B:3106:TRP:CB 1:B:3665:LEU:HD13 2.07 0.835:A:1097:ASP:O 5:A:1100:MET:N 2.10 0.83
1:B:3731:ARG:HD2 2:C:694:TRP:HE1 1.05 0.835:A:996:GLY:O 5:A:998:GLN:N 2.12 0.822:C:722:GLN:O 2:C:726:GLU:CB 2.27 0.82
7:G:140:LEU:CD1 7:G:343:GLY:N 2.42 0.821:B:2744:ASP:O 1:B:2747:THR:HG23 1.78 0.826:F:87:GLN:CG 6:F:132:MET:HE2 2.10 0.825:A:1006:SER:CB 5:A:1009:SER:CB 2.58 0.825:A:2567:VAL:C 5:A:2569:LYS:H 1.84 0.81
6:F:442:THR:HG21 6:F:448:ARG:CG 2.10 0.811:B:3404:ALA:N 1:B:3457:ILE:HG22 1.94 0.815:A:1506:LEU:C 5:A:1508:GLU:H 1.84 0.811:B:3173:THR:CB 1:B:3451:LEU:HA 2.10 0.811:B:3667:ILE:HD11 1:B:3692:VAL:CB 2.08 0.815:A:1629:GLN:O 5:A:1630:ARG:O 1.97 0.81
7:G:140:LEU:HD12 7:G:343:GLY:N 1.94 0.815:A:976:ALA:O 5:A:977:ILE:CB 2.28 0.811:B:3171:LEU:O 1:B:3174:THR:OG1 1.97 0.81
7:G:242:LEU:HD12 7:G:246:GLN:HB2 1.60 0.815:A:1361:LEU:O 5:A:1363:LEU:N 2.14 0.801:B:2633:TRP:CB 5:A:2624:LYS:C 2.50 0.801:B:3719:PHE:CA 1:B:3722:ASP:OD2 2.25 0.807:G:18:LYS:HG2 7:G:30:VAL:HG13 1.63 0.807:G:14:SER:HA 7:G:71:ILE:HB 1.62 0.805:A:976:ALA:HA 5:A:992:SER:CB 2.12 0.801:B:3106:TRP:CE3 1:B:3665:LEU:HD12 2.17 0.801:B:3253:LEU:HD12 1:B:3318:ARG:HG3 1.64 0.801:B:3493:LEU:O 1:B:3510:LYS:NZ 2.14 0.80
1:B:3466:THR:HG22 1:B:3573:HIS:HB2 1.63 0.807:G:298:VAL:HG22 7:G:330:ILE:HB 1.63 0.801:B:3169:PHE:HE1 1:B:3451:LEU:CD2 1.95 0.801:B:3656:ASP:O 1:B:3658:GLU:N 2.14 0.795:A:430:THR:O 5:A:431:VAL:C 2.21 0.79
1:B:3060:TRP:CE3 1:B:3064:ASN:ND2 2.49 0.791:B:3486:GLN:O 1:B:3486:GLN:NE2 2.16 0.79
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Page 22 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
5:A:1200:LEU:O 5:A:1203:ASP:CB 2.31 0.797:G:178:ILE:HD11 7:G:277:THR:HG21 1.65 0.791:B:3062:PHE:CZ 1:B:3657:ASN:C 2.57 0.791:B:3705:GLN:CB 1:B:3709:LEU:CB 2.61 0.786:F:87:GLN:C 6:F:132:MET:CE 2.51 0.785:A:217:SER:O 5:A:220:SER:N 2.14 0.78
1:B:3100:LEU:CD1 1:B:3101:LEU:N 2.44 0.785:A:1590:SER:O 5:A:1591:PRO:CB 2.31 0.78
1:B:2655:ILE:HG22 1:B:2656:GLU:N 1.97 0.781:B:3116:MET:O 1:B:3118:THR:N 2.16 0.78
1:B:3247:ARG:HG2 1:B:3248:LEU:H 1.49 0.785:A:1650:PHE:O 5:A:1653:SER:N 2.17 0.781:B:3555:PHE:O 1:B:3559:SER:N 2.13 0.787:G:286:ASP:CB 7:G:288:ASP:OD1 2.31 0.78
1:B:3068:LEU:CD2 1:B:3081:ALA:CB 2.53 0.781:B:3731:ARG:CZ 2:C:694:TRP:CD1 2.63 0.785:A:890:TYR:O 5:A:893:LEU:N 2.16 0.786:F:72:LYS:HB3 6:F:72:LYS:NZ 1.99 0.781:B:2853:LEU:O 1:B:2856:THR:OG1 2.02 0.781:B:3102:CYS:SG 1:B:3134:ILE:CB 2.72 0.778:E:390:ALA:O 8:E:394:TYR:N 2.16 0.77
5:A:1091:SER:CB 5:A:1099:ALA:HB1 2.15 0.771:B:2944:ALA:HA 1:B:2970:ILE:HD12 1.66 0.771:B:3068:LEU:HB3 1:B:3078:ALA:HA 1.66 0.771:B:3461:SER:CB 1:B:3464:PHE:CZ 2.67 0.777:G:140:LEU:HD12 7:G:343:GLY:H 1.49 0.775:A:2567:VAL:O 5:A:2569:LYS:N 2.18 0.773:D:140:UNK:O 6:F:178:LYS:NZ 2.15 0.776:F:71:LEU:HD12 6:F:229:LEU:HD22 1.66 0.775:A:1032:SER:O 5:A:1033:ALA:CB 2.33 0.771:B:2818:ASP:O 1:B:2821:ILE:CB 2.33 0.771:B:3496:ALA:CB 2:C:684:TYR:CE1 2.65 0.775:A:1097:ASP:O 5:A:1098:ASP:C 2.21 0.771:B:2967:LEU:O 1:B:2967:LEU:HD12 1.84 0.771:B:3047:VAL:O 1:B:3050:ASP:O 2.03 0.772:C:805:GLN:O 2:C:809:ALA:N 2.12 0.775:A:239:LYS:C 5:A:241:LEU:N 2.35 0.76
1:B:3106:TRP:CH2 1:B:3668:ARG:HG3 2.00 0.765:A:1091:SER:HA 5:A:1099:ALA:CB 2.14 0.765:A:736:PHE:N 5:A:1543:LEU:C 2.38 0.765:A:328:LEU:O 5:A:332:LEU:CB 2.33 0.76
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Page 23 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
6:F:91:GLN:HB2 6:F:132:MET:HE1 1.68 0.766:F:213:LYS:HB3 6:F:214:PRO:HD3 1.67 0.766:F:66:ARG:HH11 6:F:66:ARG:HB3 1.47 0.767:G:108:ALA:HB1 7:G:109:PRO:CD 2.15 0.765:A:1296:LEU:HA 5:A:1356:ALA:HB2 1.68 0.765:A:1605:ASN:O 5:A:1608:THR:N 2.19 0.751:B:3219:TYR:N 1:B:3220:PRO:CD 2.49 0.755:A:976:ALA:CA 5:A:992:SER:CB 2.65 0.753:D:439:UNK:O 3:D:443:UNK:N 2.19 0.757:G:150:GLY:O 7:G:293:LEU:CD2 2.33 0.757:G:19:ALA:HB3 7:G:29:ALA:HB3 1.67 0.757:G:9:VAL:O 7:G:340:TRP:NE1 2.17 0.75
6:F:87:GLN:HG3 6:F:132:MET:CE 2.16 0.757:G:102:PRO:HB3 7:G:131:ALA:HB3 1.68 0.757:G:237:GLU:HG2 7:G:251:GLY:HA2 1.68 0.756:F:213:LYS:HE3 6:F:213:LYS:CA 2.16 0.757:G:163:VAL:HG23 7:G:175:ILE:CG2 2.16 0.757:G:220:ALA:HB1 7:G:226:GLU:HG3 1.69 0.755:A:1300:ASN:C 5:A:1302:LYS:H 1.89 0.751:B:3457:ILE:O 1:B:3457:ILE:HD12 1.86 0.75
1:B:3247:ARG:NH2 1:B:3247:ARG:HG3 1.99 0.751:B:3435:GLU:OE1 1:B:3435:GLU:N 2.20 0.755:A:1255:ALA:O 5:A:1258:ASP:N 2.19 0.75
1:B:3100:LEU:HD13 1:B:3101:LEU:CA 2.16 0.751:B:3625:THR:N 1:B:3626:PRO:HD3 2.02 0.753:D:55:UNK:O 3:D:59:UNK:N 2.20 0.75
6:F:211:GLN:OE1 6:F:217:ILE:CD1 2.34 0.755:A:900:THR:CB 5:A:948:ILE:CD1 2.64 0.742:C:717:ALA:O 2:C:718:HIS:CB 2.35 0.741:B:2777:GLU:O 1:B:2781:LYS:N 2.16 0.74
1:B:3099:GLU:HB2 1:B:3425:LEU:CD1 2.08 0.741:B:3474:PHE:CD2 1:B:3526:VAL:CG2 2.58 0.741:B:3489:MET:CE 1:B:3511:VAL:HG23 2.16 0.741:B:2941:HIS:CD2 1:B:2941:HIS:H 2.04 0.741:B:3169:PHE:HE1 1:B:3451:LEU:CG 2.00 0.741:B:3404:ALA:H 1:B:3457:ILE:CG2 1.98 0.741:B:3740:PHE:CA 1:B:3742:PRO:HD3 2.17 0.745:A:1068:ASN:O 5:A:1070:ARG:N 2.21 0.74
1:B:3097:ILE:HD13 1:B:3097:ILE:N 2.03 0.743:D:419:UNK:CB 6:F:439:ILE:HD12 2.17 0.74
1:B:3171:LEU:HD23 1:B:3172:ARG:H 0.92 0.74Continued on next page...
Page 24 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3427:ASN:ND2 1:B:3428:LYS:N 2.36 0.741:B:3494:ASN:HA 1:B:3497:HIS:HB3 1.70 0.741:B:3062:PHE:HZ 1:B:3658:GLU:N 1.85 0.741:B:3244:ASP:CA 1:B:3247:ARG:HD2 2.15 0.731:B:3659:LEU:O 1:B:3662:TYR:CB 2.36 0.732:C:721:GLN:O 2:C:724:LEU:CA 2.36 0.735:A:2005:SER:O 5:A:2009:HIS:N 2.18 0.731:B:3057:TRP:O 1:B:3061:GLY:N 2.17 0.731:B:3462:VAL:O 1:B:3464:PHE:CD2 2.41 0.737:G:163:VAL:CG2 7:G:175:ILE:HD13 1.76 0.737:G:185:LEU:O 7:G:189:LEU:N 2.17 0.731:B:3492:LYS:CA 1:B:3492:LYS:HE3 2.18 0.736:F:129:LEU:N 6:F:129:LEU:HD22 2.03 0.735:A:1091:SER:C 5:A:1099:ALA:HB2 2.08 0.735:A:516:GLU:O 5:A:519:ARG:N 2.20 0.735:A:578:ASP:O 5:A:582:ASP:N 2.21 0.73
6:F:455:GLY:HA2 6:F:458:ILE:HD12 1.69 0.737:G:164:PRO:HG2 7:G:174:ALA:HB3 1.71 0.735:A:1650:PHE:O 5:A:1651:TYR:C 2.26 0.737:G:138:ALA:HB1 7:G:165:ILE:CD1 2.18 0.737:G:287:VAL:HG12 7:G:290:ARG:NH1 2.04 0.731:B:3741:MET:N 1:B:3742:PRO:HD2 2.03 0.737:G:236:ILE:O 7:G:254:ARG:NH1 2.21 0.735:A:239:LYS:O 5:A:242:THR:N 2.22 0.72
1:B:2882:GLN:HA 1:B:2885:ARG:HG3 1.70 0.721:B:3625:THR:H 1:B:3626:PRO:HD3 1.52 0.721:B:3649:SER:HB2 1:B:3705:GLN:HA 1.70 0.725:A:1069:LYS:CB 5:A:1072:TYR:CB 2.68 0.726:F:129:LEU:CD2 6:F:129:LEU:H 2.01 0.726:F:210:LYS:HB2 6:F:219:LYS:HA 1.72 0.726:F:415:SER:HA 6:F:420:LEU:HD23 1.71 0.725:A:972:LEU:O 5:A:973:ASP:O 2.07 0.721:B:3656:ASP:C 1:B:3658:GLU:H 1.92 0.725:A:1090:THR:C 5:A:1092:ILE:H 1.92 0.721:B:3062:PHE:HZ 1:B:3658:GLU:CA 2.03 0.722:C:722:GLN:C 2:C:724:LEU:N 2.38 0.725:A:856:GLU:O 5:A:860:GLU:N 2.21 0.726:F:8:VAL:HG22 8:E:368:TRP:HB3 1.70 0.724:H:57:ASN:O 4:H:61:ASN:N 2.16 0.725:A:1032:SER:O 5:A:1033:ALA:HB3 1.89 0.71
1:B:3247:ARG:HG2 1:B:3248:LEU:N 2.05 0.71Continued on next page...
Page 25 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3388:TYR:HA 1:B:3405:VAL:CB 2.20 0.711:B:3247:ARG:NH1 1:B:3407:TYR:CB 2.53 0.711:B:3424:ARG:HH12 1:B:3447:ILE:CA 1.96 0.71
6:F:92:TRP:O 6:F:96:ASN:ND2 2.23 0.715:A:410:GLU:C 5:A:412:GLU:H 1.94 0.715:A:1372:GLU:O 5:A:1373:GLU:C 2.29 0.715:A:897:GLY:O 5:A:901:LEU:N 2.18 0.71
1:B:3105:LEU:HD12 1:B:3105:LEU:O 1.91 0.711:B:3444:ASN:O 1:B:3446:PRO:HD3 1.91 0.711:B:3618:GLU:C 1:B:3620:VAL:N 2.44 0.713:D:426:UNK:O 3:D:430:UNK:N 2.22 0.713:D:440:UNK:O 3:D:444:UNK:N 2.23 0.71
1:B:3509:LEU:HD11 2:C:687:ASN:HD22 1.54 0.713:D:150:UNK:O 3:D:153:UNK:N 2.23 0.711:B:2899:ASN:N 1:B:2899:ASN:OD1 2.17 0.711:B:3169:PHE:CZ 1:B:3451:LEU:HD21 2.25 0.711:B:3424:ARG:HD3 1:B:3445:LEU:CB 2.21 0.711:B:3167:LEU:O 1:B:3167:LEU:HD12 1.90 0.713:D:151:UNK:O 3:D:155:UNK:N 2.24 0.71
1:B:2944:ALA:HA 1:B:2970:ILE:CD1 2.21 0.711:B:3644:ASN:CA 1:B:3647:THR:OG1 2.39 0.711:B:3106:TRP:CZ2 1:B:3668:ARG:HB2 2.24 0.711:B:3719:PHE:HA 1:B:3722:ASP:CG 2.09 0.716:F:444:HIS:O 6:F:445:THR:C 2.29 0.705:A:583:ALA:O 5:A:587:TYR:N 2.23 0.70
1:B:3375:LEU:CB 1:B:3376:PRO:CD 2.68 0.706:F:212:ARG:O 6:F:275:ASN:ND2 2.20 0.70
1:B:3169:PHE:HE1 1:B:3451:LEU:HG 1.56 0.701:B:3427:ASN:N 1:B:3443:PHE:CE1 2.58 0.70
6:F:442:THR:HG22 6:F:448:ARG:HE 1.49 0.707:G:151:ILE:CG2 7:G:297:ILE:HA 2.21 0.705:A:1093:LYS:C 5:A:1095:LEU:H 1.92 0.701:B:3086:LEU:N 1:B:3104:ILE:HD13 2.07 0.705:A:2415:ARG:O 5:A:2419:PRO:N 2.24 0.705:A:814:THR:O 5:A:818:SER:N 2.18 0.701:B:3418:ARG:O 1:B:3422:LEU:HD21 1.90 0.706:F:87:GLN:HG2 6:F:132:MET:CE 2.21 0.705:A:410:GLU:C 5:A:412:GLU:N 2.45 0.705:A:1090:THR:O 5:A:1092:ILE:N 2.25 0.705:A:1605:ASN:O 5:A:1607:VAL:N 2.24 0.705:A:2243:ILE:CB 5:A:2253:VAL:CA 2.69 0.70
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Page 26 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3618:GLU:O 1:B:3620:VAL:C 2.28 0.707:G:132:PHE:N 7:G:357:ILE:O 2.25 0.705:A:2389:SER:O 5:A:2392:LYS:N 2.25 0.706:F:204:ILE:HB 6:F:274:TRP:CE3 2.26 0.705:A:1605:ASN:O 5:A:1606:PRO:C 2.27 0.701:B:3168:HIS:O 1:B:3172:ARG:N 2.25 0.702:C:754:ARG:O 2:C:758:ALA:N 2.24 0.701:B:3646:PHE:O 1:B:3649:SER:OG 2.08 0.70
1:B:3667:ILE:HD13 1:B:3692:VAL:CA 2.21 0.703:D:172:UNK:N 8:E:357:THR:OG1 2.25 0.696:F:87:GLN:CG 6:F:132:MET:HE1 2.22 0.697:G:124:PHE:CZ 7:G:132:PHE:HB3 2.27 0.69
1:B:3101:LEU:HD22 1:B:3101:LEU:O 1.92 0.691:B:3391:LEU:H 1:B:3402:SER:CB 2.03 0.695:A:1964:ASP:O 5:A:1968:ASN:N 2.21 0.695:A:1859:LEU:O 5:A:1860:PHE:C 2.29 0.691:B:3094:ASN:CB 1:B:3097:ILE:HG12 2.22 0.691:B:3253:LEU:CD1 1:B:3318:ARG:HG3 2.22 0.692:C:699:ARG:HD2 2:C:699:ARG:N 2.04 0.697:G:163:VAL:HG22 7:G:175:ILE:HG12 0.99 0.697:G:9:VAL:HG21 7:G:344:SER:HA 1.75 0.691:B:3173:THR:O 1:B:3452:SER:HB2 1.93 0.695:A:2181:MET:O 5:A:2185:PRO:N 2.26 0.691:B:2914:ASN:OD1 1:B:2915:ALA:N 2.25 0.695:A:900:THR:CB 5:A:948:ILE:HD13 2.23 0.691:B:3737:ASP:OD2 1:B:3739:ASN:ND2 2.26 0.696:F:428:LEU:CB 6:F:437:PHE:HE2 2.05 0.691:B:3422:LEU:H 1:B:3422:LEU:CD2 2.06 0.691:B:2638:ASN:C 1:B:2642:SER:HB3 2.13 0.691:B:2962:VAL:HA 1:B:2965:SER:HB3 1.74 0.697:G:297:ILE:HB 7:G:329:ILE:HG13 1.76 0.681:B:2670:GLN:N 1:B:2837:PRO:CG 2.56 0.687:G:212:ILE:HG23 7:G:216:LEU:HD12 1.74 0.681:B:2817:CYS:CB 1:B:2852:PHE:HZ 2.07 0.68
1:B:3068:LEU:HD23 1:B:3081:ALA:HB1 1.71 0.681:B:3670:GLU:O 1:B:3673:SER:OG 2.12 0.684:H:12:GLN:O 4:H:16:THR:N 2.27 0.685:A:369:TYR:O 5:A:373:GLU:N 2.26 0.686:F:1:MET:H 7:G:371:HIS:CG 2.12 0.685:A:1292:ILE:C 5:A:1294:CYS:N 2.36 0.687:G:121:GLN:O 7:G:362:TYR:OH 2.12 0.68
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Page 27 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
5:A:516:GLU:O 5:A:517:PHE:C 2.30 0.681:B:3489:MET:HE1 1:B:3511:VAL:HG23 1.75 0.681:B:3568:THR:CB 1:B:3569:PRO:HD2 2.07 0.681:B:3644:ASN:O 1:B:3647:THR:OG1 2.09 0.681:B:3055:LYS:C 1:B:3059:GLN:HB2 2.13 0.681:B:3625:THR:N 1:B:3626:PRO:CD 2.56 0.685:A:967:THR:O 5:A:968:GLU:O 2.11 0.675:A:976:ALA:C 5:A:992:SER:CB 2.62 0.671:B:3514:PHE:O 1:B:3518:GLN:N 2.22 0.677:G:151:ILE:CG2 7:G:297:ILE:HG12 2.24 0.675:A:2243:ILE:CB 5:A:2253:VAL:HA 2.24 0.671:B:3468:HIS:HB2 1:B:3570:HIS:HA 1.77 0.674:H:261:ARG:O 4:H:265:PHE:N 2.28 0.678:E:382:ALA:O 8:E:385:THR:OG1 2.11 0.677:G:24:ASP:HB2 7:G:340:TRP:HH2 1.60 0.675:A:1249:GLN:O 5:A:1251:GLU:N 2.24 0.672:C:713:LYS:O 2:C:714:GLY:C 2.32 0.675:A:2243:ILE:CB 5:A:2252:SER:CB 2.72 0.671:B:3481:ASP:CB 1:B:3482:PRO:HD2 2.24 0.671:B:3649:SER:CB 1:B:3704:ALA:O 2.43 0.67
1:B:3105:LEU:HD12 1:B:3105:LEU:C 2.15 0.672:C:684:TYR:HA 2:C:687:ASN:HB3 1.76 0.671:B:2670:GLN:HA 1:B:2837:PRO:HG3 1.72 0.671:B:3407:TYR:N 1:B:3408:PRO:HD2 2.04 0.676:F:11:GLY:N 6:F:461:SER:O 2.26 0.676:F:233:ALA:O 6:F:237:GLY:N 2.27 0.677:G:137:GLN:N 7:G:137:GLN:OE1 2.27 0.67
5:A:1345:LEU:HA 5:A:1349:MET:CB 2.25 0.677:G:347:ALA:O 7:G:353:GLN:NE2 2.27 0.67
7:G:163:VAL:HG21 7:G:175:ILE:HD11 1.58 0.671:B:3448:ALA:HA 1:B:3458:MET:HA 1.77 0.671:B:3667:ILE:HD13 1:B:3692:VAL:C 2.14 0.671:B:3060:TRP:CZ3 1:B:3064:ASN:ND2 2.62 0.665:A:486:MET:O 5:A:490:GLY:N 2.28 0.66
1:B:3169:PHE:CE1 1:B:3451:LEU:CD2 2.73 0.667:G:312:ARG:NE 7:G:316:GLU:OE2 2.18 0.663:D:156:UNK:O 3:D:160:UNK:N 2.28 0.667:G:242:LEU:N 7:G:246:GLN:O 2.26 0.661:B:3019:LYS:CG 1:B:3020:ALA:N 2.58 0.661:B:3461:SER:CB 1:B:3464:PHE:HZ 2.06 0.667:G:275:ASP:OD1 7:G:276:GLN:N 2.24 0.66
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Page 28 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:2633:TRP:CB 5:A:2624:LYS:CA 2.73 0.664:H:113:LEU:O 4:H:117:LYS:N 2.24 0.665:A:1093:LYS:C 5:A:1095:LEU:N 2.48 0.665:A:353:HIS:O 5:A:357:THR:N 2.25 0.666:F:47:TYR:O 6:F:53:ASN:OD1 2.13 0.66
6:F:174:MET:HA 6:F:489[B]:ARG:HB3 1.78 0.667:G:239:SER:HA 7:G:249:THR:HA 1.78 0.665:A:588:ARG:O 5:A:592:SER:N 2.17 0.661:B:3060:TRP:O 1:B:3063:PHE:N 2.28 0.661:B:3527:LEU:O 1:B:3531:PHE:N 2.25 0.661:B:3719:PHE:C 1:B:3722:ASP:HB2 2.15 0.667:G:99:GLU:HA 7:G:129:VAL:HA 1.78 0.661:B:3062:PHE:CZ 1:B:3657:ASN:O 2.49 0.66
1:B:3253:LEU:HD11 1:B:3318:ARG:HB2 1.78 0.662:C:695:GLN:O 2:C:699:ARG:HD3 1.96 0.653:D:64:UNK:O 6:F:434:SER:OG 2.06 0.65
3:D:396:UNK:HA 6:F:436:LYS:HE3 1.78 0.656:F:72:LYS:HD2 6:F:73:PRO:HD2 1.77 0.65
1:B:3101:LEU:HD13 1:B:3101:LEU:C 2.15 0.655:A:1296:LEU:HA 5:A:1356:ALA:CB 2.26 0.651:B:3086:LEU:N 1:B:3104:ILE:CD1 2.58 0.651:B:3423:TYR:CB 1:B:3558:MET:CE 2.74 0.656:F:169:PRO:HB2 6:F:176:LEU:HB2 1.79 0.657:G:163:VAL:HG23 7:G:175:ILE:HG23 1.78 0.655:A:1646:ASN:O 5:A:1649:ASP:N 2.30 0.655:A:1763:LYS:O 5:A:1767:PHE:N 2.30 0.65
1:B:3494:ASN:HD22 1:B:3497:HIS:HB3 1.61 0.651:B:3101:LEU:HD13 1:B:3101:LEU:O 1.96 0.655:A:1036:PRO:O 5:A:1038:ASN:N 2.29 0.655:A:1201:CYS:HA 5:A:1209:LYS:HA 1.79 0.655:A:1452:SER:O 5:A:1456:ILE:N 2.30 0.655:A:424:ASP:C 5:A:426:SER:N 2.50 0.651:B:3437:ARG:O 1:B:3440:SER:N 2.28 0.65
1:B:2748:GLU:HB3 1:B:2752:HIS:HD2 1.59 0.651:B:3241:THR:O 1:B:3242:ASP:CB 2.43 0.651:B:3541:PHE:O 1:B:3544:PHE:N 2.25 0.654:H:115:ASP:O 4:H:119:ASP:N 2.24 0.654:H:183:LYS:O 4:H:187:LEU:N 2.27 0.651:B:2998:GLU:O 1:B:3001:THR:N 2.30 0.64
1:B:2635:GLN:OE1 1:B:2635:GLN:N 2.28 0.646:F:191:ASN:HA 6:F:194:ILE:HD12 1.79 0.64
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Page 29 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
6:F:254:THR:O 6:F:258:THR:N 2.29 0.641:B:2821:ILE:CB 1:B:2849:TYR:HE2 2.06 0.64
1:B:3100:LEU:HD13 1:B:3100:LEU:C 2.17 0.641:B:3509:LEU:HA 1:B:3512:GLU:HB3 1.79 0.64
1:B:3253:LEU:HD21 1:B:3314:LEU:CA 2.27 0.641:B:2967:LEU:HD12 1:B:2967:LEU:C 2.17 0.641:B:3062:PHE:CZ 1:B:3658:GLU:CA 2.80 0.647:G:138:ALA:CB 7:G:165:ILE:CD1 2.69 0.645:A:1247:ASP:O 5:A:1248:THR:CB 2.44 0.645:A:2243:ILE:CB 5:A:2252:SER:O 2.46 0.641:B:3159:ILE:O 1:B:3163:TYR:N 2.31 0.64
1:B:3427:ASN:HD22 1:B:3428:LYS:N 1.94 0.645:A:1152:ALA:C 5:A:1154:SER:H 1.97 0.645:A:217:SER:O 5:A:219:PHE:N 2.30 0.645:A:389:PRO:O 5:A:392:TYR:N 2.30 0.645:A:483:ASP:O 5:A:487:LYS:N 2.30 0.641:B:2691:GLY:O 1:B:2695:GLU:N 2.31 0.641:B:3509:LEU:O 1:B:3513:ILE:N 2.27 0.641:B:3652:LEU:C 1:B:3652:LEU:HD22 2.17 0.645:A:122:LEU:CB 5:A:219:PHE:CB 2.75 0.635:A:579:PRO:O 5:A:583:ALA:N 2.31 0.637:G:138:ALA:HA 7:G:152:VAL:CG1 2.28 0.634:H:189:ARG:O 4:H:193:LEU:N 2.20 0.635:A:1091:SER:O 5:A:1099:ALA:HB2 1.98 0.635:A:976:ALA:O 5:A:992:SER:CB 2.46 0.63
1:B:3100:LEU:HD22 1:B:3100:LEU:C 2.17 0.631:B:3171:LEU:C 1:B:3174:THR:HG1 2.00 0.63
1:B:3474:PHE:HE2 1:B:3526:VAL:HG21 0.93 0.635:A:1117:THR:O 5:A:1121:ASN:N 2.29 0.631:B:2651:ASN:O 1:B:2654:ILE:N 2.31 0.631:B:3646:PHE:CB 1:B:3720:ILE:HD11 2.28 0.633:D:278:UNK:O 3:D:282:UNK:N 2.31 0.636:F:16:ALA:HB2 6:F:107:PRO:HG2 1.80 0.636:F:71:LEU:CD1 6:F:229:LEU:HD22 2.29 0.635:A:686:LEU:O 5:A:690:PHE:N 2.20 0.63
6:F:107:PRO:HB2 6:F:469:TRP:CZ3 2.34 0.635:A:1580:LEU:O 5:A:1583:LYS:CB 2.47 0.636:F:213:LYS:HE3 6:F:213:LYS:HA 1.80 0.636:F:266:ALA:C 6:F:282:ASN:HD21 2.01 0.631:B:2779:SER:O 1:B:2783:VAL:N 2.27 0.631:B:2651:ASN:O 1:B:2652:THR:C 2.37 0.62
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Page 30 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3040:ASN:OD1 1:B:3060:TRP:CZ2 2.52 0.621:B:3229:LEU:HD12 1:B:3229:LEU:C 2.18 0.621:B:3462:VAL:O 1:B:3464:PHE:N 2.32 0.62
1:B:3740:PHE:HB3 1:B:3742:PRO:HD3 1.80 0.623:D:277:UNK:O 3:D:281:UNK:N 2.31 0.622:C:673:SER:O 2:C:675:HIS:N 2.32 0.627:G:73:HIS:HA 7:G:159:VAL:HG13 1.82 0.624:H:24:GLU:O 4:H:28:ASN:N 2.27 0.625:A:430:THR:C 5:A:432:GLN:N 2.53 0.621:B:2961:ASP:C 1:B:2963:CYS:N 2.48 0.621:B:3493:LEU:C 1:B:3493:LEU:HD13 2.19 0.621:B:3703:VAL:C 1:B:3704:ALA:O 2.36 0.621:B:3244:ASP:O 1:B:3247:ARG:CG 2.45 0.621:B:3474:PHE:CG 1:B:3526:VAL:CG1 2.75 0.627:G:163:VAL:HG23 7:G:175:ILE:CB 2.28 0.627:G:273:GLY:O 7:G:277:THR:N 2.28 0.625:A:1069:LYS:O 5:A:1070:ARG:C 2.37 0.625:A:487:LYS:O 5:A:491:ARG:N 2.17 0.62
7:G:151:ILE:HG23 7:G:151:ILE:O 2.00 0.625:A:137:LEU:O 5:A:138:ASP:C 2.37 0.62
6:F:413:GLY:HA3 6:F:449:GLN:HE21 1.64 0.625:A:217:SER:O 5:A:218:MET:C 2.38 0.625:A:2256:GLY:O 5:A:2260:ALA:N 2.28 0.625:A:424:ASP:C 5:A:426:SER:H 2.03 0.62
1:B:2912:ILE:HD13 1:B:2912:ILE:N 2.14 0.621:B:3492:LYS:HD2 1:B:3492:LYS:N 2.14 0.626:F:112:GLU:OE1 6:F:116:ASN:ND2 2.24 0.626:F:301:PRO:HG2 6:F:304:TRP:HB2 1.81 0.625:A:1506:LEU:C 5:A:1508:GLU:N 2.51 0.621:B:3055:LYS:CB 1:B:3059:GLN:CG 2.78 0.621:B:3404:ALA:O 1:B:3457:ILE:CG2 2.48 0.624:H:191:THR:O 4:H:195:LYS:N 2.33 0.624:H:51:GLN:O 4:H:54:LEU:N 2.32 0.625:A:1036:PRO:C 5:A:1038:ASN:H 2.02 0.621:B:2822:GLN:O 1:B:2824:SER:N 2.32 0.625:A:1090:THR:C 5:A:1092:ILE:N 2.53 0.615:A:346:GLU:O 5:A:350:ALA:N 2.25 0.613:D:161:UNK:O 3:D:166:UNK:N 2.33 0.61
5:A:897:GLY:HA2 5:A:948:ILE:HD11 1.81 0.611:B:3116:MET:O 1:B:3117:LEU:C 2.38 0.617:G:131:ALA:HA 7:G:358:SER:HA 1.82 0.61
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Page 31 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3489:MET:HE1 1:B:3511:VAL:CG2 2.30 0.613:D:74:UNK:O 3:D:75:UNK:CB 2.48 0.618:E:360:ASN:O 8:E:364:GLU:HG3 1.99 0.616:F:32:GLY:HA2 8:E:373:PHE:HZ 1.65 0.611:B:3418:ARG:O 1:B:3422:LEU:HD22 1.99 0.61
1:B:3422:LEU:HD22 1:B:3422:LEU:N 2.09 0.612:C:739:SER:HA 3:D:328:UNK:O 2.01 0.615:A:1859:LEU:C 5:A:1861:ARG:N 2.53 0.61
1:B:2885:ARG:HD3 1:B:2885:ARG:C 2.20 0.611:B:3068:LEU:HD22 1:B:3081:ALA:HB3 1.79 0.611:B:3492:LYS:HA 1:B:3492:LYS:CE 2.28 0.612:C:721:GLN:O 2:C:724:LEU:N 2.32 0.613:D:168:UNK:O 3:D:171:UNK:N 2.34 0.616:F:80:VAL:HB 6:F:83:TRP:CZ2 2.36 0.61
7:G:150:GLY:HA3 7:G:296:ASN:HB2 1.81 0.614:H:119:ASP:O 4:H:122:LYS:N 2.30 0.61
1:B:3418:ARG:HH11 1:B:3418:ARG:CG 2.14 0.616:F:153:PRO:HB3 8:E:363:LEU:HD13 1.82 0.611:B:2651:ASN:H 1:B:2651:ASN:ND2 1.98 0.616:F:71:LEU:HD11 6:F:229:LEU:CD1 2.25 0.617:G:139:VAL:N 7:G:165:ILE:HD13 2.16 0.614:H:25:LEU:O 4:H:29:GLY:N 2.27 0.61
1:B:3062:PHE:HZ 1:B:3657:ASN:O 1.83 0.616:F:72:LYS:HZ3 6:F:72:LYS:HB3 1.63 0.611:B:3354:ILE:CB 1:B:3355:PRO:CD 2.79 0.611:B:3427:ASN:HA 1:B:3443:PHE:HZ 1.58 0.611:B:3062:PHE:CZ 1:B:3658:GLU:N 2.69 0.617:G:149:THR:HG23 7:G:166:TYR:HA 1.83 0.61
7:G:19:ALA:N 7:G:29:ALA:O 2.34 0.614:H:231:SER:O 4:H:235:LEU:N 2.33 0.616:F:272:SER:OG 6:F:276:GLU:N 2.33 0.616:F:446:ILE:H 6:F:446:ILE:HD12 1.64 0.616:F:87:GLN:CA 6:F:132:MET:HE2 2.31 0.616:F:8:VAL:HG21 8:E:368:TRP:O 2.01 0.61
1:B:3101:LEU:HD22 1:B:3104:ILE:HB 1.81 0.601:B:3106:TRP:CZ2 1:B:3668:ARG:HB3 2.32 0.60
7:G:9:VAL:N 7:G:20:GLY:O 2.25 0.601:B:2895:VAL:HG12 1:B:2895:VAL:O 2.02 0.601:B:3489:MET:HE2 1:B:3511:VAL:HG23 1.83 0.601:B:3556:VAL:O 1:B:3559:SER:OG 2.11 0.607:G:107:GLU:HB2 7:G:111:ASN:HD22 1.65 0.60
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Page 32 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
7:G:7:ALA:O 7:G:22:ALA:N 2.33 0.601:B:2636:SER:HA 1:B:2639:ILE:HG13 1.83 0.601:B:3394:ARG:HA 1:B:3398:GLY:HA2 1.83 0.608:E:366:ALA:C 8:E:368:TRP:H 2.05 0.605:A:1938:ALA:O 5:A:1942:VAL:N 2.31 0.601:B:3019:LYS:HG3 1:B:3020:ALA:N 2.17 0.601:B:3139:GLN:CB 1:B:3418:ARG:CZ 2.76 0.606:F:308:ASN:OD1 6:F:309:SER:N 2.34 0.607:G:33:SER:O 7:G:33:SER:OG 2.18 0.605:A:976:ALA:O 5:A:992:SER:CA 2.50 0.605:A:634:PHE:O 5:A:638:PHE:N 2.33 0.605:A:872:LEU:O 5:A:876:LEU:N 2.28 0.60
1:B:3068:LEU:HD12 1:B:3069:SER:N 2.17 0.601:B:3423:TYR:CB 1:B:3558:MET:HE2 2.32 0.601:B:3071:GLU:O 1:B:3072:PRO:O 2.19 0.602:C:739:SER:CB 3:D:328:UNK:O 2.49 0.607:G:147:ARG:NE 7:G:296:ASN:OD1 2.34 0.605:A:995:PRO:CB 5:A:2558:ARG:CB 2.80 0.605:A:878:PHE:O 5:A:881:LYS:N 2.34 0.60
1:B:3169:PHE:CE1 1:B:3451:LEU:CG 2.85 0.601:B:3577:THR:O 5:A:965:ASP:N 2.35 0.607:G:150:GLY:O 7:G:293:LEU:HD23 2.02 0.605:A:2389:SER:O 5:A:2390:LEU:C 2.39 0.601:B:2638:ASN:O 1:B:2642:SER:CA 2.49 0.601:B:2690:ILE:CB 1:B:3715:VAL:CB 2.80 0.601:B:3423:TYR:CB 1:B:3558:MET:HE1 2.32 0.595:A:682:LEU:O 5:A:686:LEU:N 2.25 0.591:B:3441:ILE:O 1:B:3441:ILE:HG22 2.01 0.598:E:370:GLN:O 8:E:374:LYS:N 2.25 0.596:F:66:ARG:HB3 6:F:66:ARG:CZ 2.32 0.597:G:34:ILE:HD12 7:G:55:GLY:O 2.02 0.591:B:3169:PHE:CE1 1:B:3451:LEU:HG 2.37 0.591:B:3544:PHE:HE1 1:B:3579:GLY:HA2 1.67 0.596:F:171:VAL:O 6:F:174:MET:N 2.26 0.595:A:976:ALA:O 5:A:992:SER:HA 2.02 0.591:B:2970:ILE:O 1:B:2970:ILE:HG22 2.00 0.597:G:353:GLN:HA 7:G:356:TRP:CD1 2.38 0.595:A:1646:ASN:O 5:A:1647:PHE:C 2.39 0.595:A:914:ASP:O 5:A:917:ILE:N 2.35 0.59
1:B:2643:ILE:HG23 1:B:2643:ILE:O 2.00 0.596:F:91:GLN:H 6:F:132:MET:HE3 1.68 0.59
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Page 33 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
6:F:99:TYR:OH 7:G:177:ARG:NH1 2.36 0.595:A:430:THR:O 5:A:433:ILE:N 2.35 0.591:B:2670:GLN:C 1:B:2837:PRO:HG3 2.23 0.591:B:2835:TYR:O 1:B:2839:HIS:N 2.35 0.591:B:3085:TYR:CB 1:B:3104:ILE:CD1 2.81 0.596:F:442:THR:HG21 6:F:448:ARG:CD 2.33 0.597:G:192:ILE:HD12 7:G:253:GLU:HG2 1.84 0.597:G:287:VAL:HG23 7:G:287:VAL:O 2.02 0.595:A:1091:SER:O 5:A:1099:ALA:CB 2.51 0.595:A:982:ILE:CB 5:A:2481:ASN:CA 2.80 0.59
1:B:3366:VAL:HG13 1:B:3366:VAL:O 2.02 0.596:F:171:VAL:HG11 6:F:400:LEU:HD13 1.84 0.591:B:3664:ALA:O 1:B:3667:ILE:HG13 2.03 0.585:A:894:VAL:O 5:A:897:GLY:N 2.33 0.585:A:1107:LEU:O 5:A:1111:CYS:N 2.36 0.585:A:474:ARG:O 5:A:478:LEU:N 2.35 0.585:A:594:LEU:O 5:A:597:ILE:N 2.36 0.58
6:F:211:GLN:HB2 6:F:217:ILE:HD12 1.84 0.587:G:172:PRO:HA 7:G:175:ILE:HD12 1.85 0.581:B:3097:ILE:O 1:B:3097:ILE:HG22 2.02 0.586:F:213:LYS:CE 6:F:213:LYS:HA 2.33 0.586:F:230:TYR:O 6:F:234:ASN:ND2 2.36 0.587:G:5:VAL:HB 7:G:101:HIS:CE1 2.37 0.587:G:159:VAL:HB 7:G:179:ASP:HA 1.83 0.581:B:3547:GLN:O 1:B:3551:GLN:N 2.31 0.587:G:357:ILE:HA 7:G:361:GLU:OE1 2.04 0.585:A:927:ALA:O 5:A:930:ASN:OD1 2.21 0.58
1:B:2851:GLU:HA 1:B:2854:GLU:HB2 1.85 0.581:B:2817:CYS:CB 1:B:2852:PHE:CE2 2.86 0.581:B:3106:TRP:HZ3 1:B:3668:ARG:CD 1.91 0.581:B:3483:ASP:N 1:B:3483:ASP:OD1 2.34 0.587:G:144:SER:OG 7:G:338:SER:HB3 2.04 0.585:A:341:SER:O 5:A:345:LYS:N 2.33 0.581:B:3354:ILE:CB 1:B:3369:ILE:O 2.51 0.586:F:116:ASN:OD1 6:F:117:SER:N 2.37 0.584:H:109:ASP:O 4:H:113:LEU:N 2.22 0.585:A:1372:GLU:C 5:A:1374:LEU:N 2.57 0.581:B:3644:ASN:C 1:B:3647:THR:OG1 2.42 0.586:F:94:LEU:O 6:F:100:LEU:N 2.35 0.58
1:B:2844:HIS:HA 1:B:2847:GLN:HB3 1.86 0.581:B:3404:ALA:C 1:B:3457:ILE:HG22 2.24 0.58
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Page 34 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
5:A:2601:ASN:O 5:A:2604:ASN:N 2.37 0.581:B:3421:GLN:OE1 1:B:3421:GLN:N 2.37 0.583:D:286:UNK:O 3:D:290:UNK:N 2.37 0.586:F:87:GLN:HA 6:F:132:MET:HE2 1.86 0.587:G:335:ARG:HA 7:G:338:SER:OG 2.04 0.587:G:139:VAL:HG13 7:G:165:ILE:CG2 2.29 0.576:F:58:SER:HB2 6:F:92:TRP:HH2 1.69 0.577:G:79:TRP:HZ2 7:G:115:ASN:OD1 1.85 0.576:F:444:HIS:O 6:F:446:ILE:CA 2.52 0.57
6:F:483:LEU:HG 6:F:487:ARG:HH12 1.70 0.575:A:1373:GLU:O 5:A:1377:LEU:N 2.34 0.571:B:3168:HIS:O 1:B:3172:ARG:CB 2.49 0.57
1:B:3515:ASN:ND2 1:B:3733:LEU:HD22 2.20 0.576:F:261:GLU:O 6:F:265:THR:HB 2.05 0.576:F:70:GLU:HG2 6:F:70:GLU:O 2.04 0.575:A:1581:GLU:O 5:A:1585:ARG:CA 2.52 0.57
1:B:3229:LEU:HD12 1:B:3229:LEU:O 2.02 0.576:F:210:LYS:HB3 6:F:217:ILE:HG22 1.85 0.575:A:2179:TRP:O 5:A:2183:ASN:N 2.28 0.575:A:2369:VAL:O 5:A:2370:LYS:C 2.42 0.575:A:2410:THR:O 5:A:2414:VAL:N 2.35 0.571:B:2941:HIS:N 1:B:2941:HIS:CD2 2.73 0.573:D:172:UNK:O 3:D:176:UNK:N 2.38 0.575:A:1097:ASP:C 5:A:1099:ALA:N 2.58 0.571:B:3054:ALA:O 1:B:3055:LYS:C 2.43 0.57
1:B:3740:PHE:HB2 1:B:3742:PRO:HD3 1.85 0.576:F:25:THR:HG22 6:F:41:PRO:HA 1.87 0.576:F:83:TRP:HB3 6:F:127:VAL:HG21 1.87 0.573:D:185:UNK:O 6:F:9:TYR:N 2.38 0.577:G:279:TYR:CZ 7:G:283:MET:HG3 2.40 0.577:G:137:GLN:HG3 7:G:339:VAL:HG11 1.87 0.577:G:349:LEU:HB2 7:G:352:PHE:HB3 1.86 0.571:B:2637:ILE:HG13 1:B:2665:LEU:HD12 1.86 0.571:B:2943:ILE:C 1:B:2970:ILE:HD11 2.25 0.57
7:G:250:ILE:HG22 7:G:254:ARG:HG3 1.87 0.571:B:3576:LYS:CD 1:B:3576:LYS:H 2.13 0.571:B:3503:ALA:HB1 1:B:3506:MET:HB2 1.87 0.566:F:10:GLY:HA2 6:F:463:GLY:H 1.69 0.566:F:87:GLN:CA 6:F:132:MET:CE 2.82 0.566:F:148:PHE:HD2 6:F:459:LEU:HD11 1.70 0.567:G:238:LYS:O 7:G:250:ILE:N 2.38 0.56
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Page 35 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
7:G:34:ILE:HG12 7:G:69:TYR:CE1 2.39 0.561:B:3055:LYS:O 1:B:3056:ALA:C 2.43 0.56
1:B:3489:MET:CE 1:B:3511:VAL:CG2 2.83 0.565:A:1295:GLU:O 5:A:1356:ALA:HB1 2.04 0.56
1:B:3555:PHE:HB2 1:B:3558:MET:HB3 1.87 0.562:C:715:PRO:O 2:C:716:ARG:C 2.43 0.561:B:2964:ILE:N 1:B:2964:ILE:HD13 2.19 0.56
1:B:3171:LEU:CG 1:B:3172:ARG:N 2.69 0.566:F:120:ASN:HA 6:F:123:LYS:HB3 1.88 0.567:G:8:LEU:HD12 7:G:103:VAL:HG22 1.87 0.566:F:170:ILE:HD13 6:F:175:THR:HA 1.87 0.561:B:2847:GLN:OE1 1:B:2847:GLN:HA 2.04 0.566:F:462:LEU:HD21 8:E:369:MET:HB2 1.88 0.567:G:36:GLY:HA3 7:G:67:LEU:HD23 1.88 0.565:A:2524:LYS:O 5:A:2528:ALA:N 2.38 0.56
1:B:3068:LEU:HB3 1:B:3078:ALA:CA 2.36 0.563:D:79:UNK:O 3:D:80:UNK:C 2.50 0.56
7:G:287:VAL:HG12 7:G:290:ARG:CZ 2.35 0.561:B:2651:ASN:H 1:B:2651:ASN:HD22 1.54 0.561:B:3085:TYR:CA 1:B:3104:ILE:HD11 2.35 0.561:B:3568:THR:CG2 1:B:3569:PRO:CD 2.75 0.565:A:1152:ALA:C 5:A:1154:SER:N 2.57 0.561:B:2991:CYS:CB 1:B:2999:LEU:CB 2.83 0.561:B:3089:ALA:HB1 1:B:3100:LEU:HD11 1.88 0.567:G:300:SER:N 7:G:304:THR:HG21 2.20 0.565:A:1036:PRO:C 5:A:1038:ASN:N 2.59 0.561:B:2849:TYR:HA 1:B:2852:PHE:HB3 1.87 0.561:B:3068:LEU:CB 1:B:3078:ALA:HB2 2.33 0.561:B:3106:TRP:CZ3 1:B:3668:ARG:NH2 2.74 0.561:B:3354:ILE:HA 1:B:3371:ILE:N 2.15 0.561:B:3432:LYS:HB2 1:B:3432:LYS:NZ 2.21 0.561:B:3517:ILE:O 1:B:3521:PHE:N 2.36 0.566:F:213:LYS:HE3 6:F:213:LYS:O 2.05 0.561:B:3366:VAL:O 1:B:3367:HIS:O 2.24 0.551:B:3437:ARG:C 1:B:3440:SER:H 2.09 0.551:B:3573:HIS:HB3 1:B:3582:PHE:HB3 1.87 0.556:F:44:TYR:HB3 6:F:74:ILE:HD11 1.88 0.557:G:58:ALA:HB1 7:G:67:LEU:HD22 1.87 0.551:B:3055:LYS:O 1:B:3059:GLN:HB2 2.06 0.55
1:B:3085:TYR:CB 1:B:3104:ILE:HD11 2.36 0.555:A:424:ASP:O 5:A:425:GLU:C 2.45 0.55
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Page 36 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3015:GLY:HA2 1:B:3019:LYS:HB3 1.88 0.556:F:245:THR:OG1 6:F:246:LEU:HD12 2.05 0.557:G:187:ASP:O 7:G:191:LYS:HG3 2.07 0.552:C:797:ALA:O 2:C:801:LEU:N 2.39 0.556:F:266:ALA:O 6:F:282:ASN:ND2 2.34 0.556:F:87:GLN:C 6:F:132:MET:HE1 2.25 0.551:B:3462:VAL:C 1:B:3464:PHE:H 2.10 0.557:G:6:ALA:O 7:G:101:HIS:ND1 2.34 0.55
5:A:591:MET:O 5:A:595:LYS:N 2.23 0.557:G:27:PRO:HB3 7:G:340:TRP:CE2 2.42 0.555:A:1103:LEU:C 5:A:1105:ASN:H 2.09 0.555:A:1372:GLU:O 5:A:1374:LEU:CA 2.54 0.556:F:308:ASN:HA 6:F:382:LEU:H 1.71 0.557:G:16:MET:O 7:G:18:LYS:HG3 2.06 0.557:G:150:GLY:O 7:G:293:LEU:HD22 2.07 0.555:A:681:GLU:O 5:A:685:TYR:N 2.26 0.551:B:3085:TYR:O 1:B:3104:ILE:HD11 2.06 0.557:G:332:PRO:HD2 7:G:335:ARG:HB3 1.88 0.555:A:2564:PHE:CB 5:A:2607:LEU:O 2.55 0.551:B:2822:GLN:O 1:B:2823:LEU:C 2.44 0.55
1:B:3023:PHE:HB3 1:B:3046:ALA:HB1 1.89 0.551:B:3375:LEU:CB 1:B:3376:PRO:HD2 2.37 0.551:B:3656:ASP:C 1:B:3658:GLU:N 2.59 0.555:A:1372:GLU:O 5:A:1374:LEU:C 2.44 0.545:A:2567:VAL:C 5:A:2569:LYS:N 2.52 0.541:B:2797:PHE:HA 1:B:2852:PHE:HE1 1.71 0.541:B:3217:THR:HA 1:B:3220:PRO:HG3 1.89 0.541:B:3717:THR:O 1:B:3720:ILE:HB 2.06 0.541:B:3741:MET:N 1:B:3742:PRO:HD3 2.00 0.547:G:286:ASP:HB2 7:G:288:ASP:OD2 2.08 0.547:G:108:ALA:HB1 7:G:109:PRO:HD2 1.89 0.547:G:330:ILE:HG22 7:G:332:PRO:HD3 1.89 0.541:B:3062:PHE:CZ 1:B:3658:GLU:CB 2.91 0.547:G:10:ILE:HA 7:G:19:ALA:HA 1.88 0.547:G:84:LYS:HA 7:G:87:HIS:HB3 1.90 0.547:G:54:VAL:HB 7:G:88:HIS:CG 2.42 0.541:B:2634:TYR:N 1:B:2634:TYR:CD1 2.75 0.541:B:3731:ARG:CD 2:C:694:TRP:CD1 2.88 0.546:F:458:ILE:HG12 8:E:373:PHE:HD2 1.72 0.541:B:3479:GLY:O 1:B:3480:PHE:O 2.26 0.541:B:3712:THR:CB 1:B:3713:PRO:HD2 2.37 0.54
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Page 37 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
6:F:20:ASP:OD2 6:F:452:SER:OG 2.18 0.547:G:107:GLU:HB3 7:G:134:VAL:HG11 1.89 0.545:A:1090:THR:O 5:A:1093:LYS:N 2.39 0.545:A:2225:ILE:HA 5:A:2229:GLU:CB 2.38 0.545:A:580:ILE:HA 5:A:583:ALA:CB 2.38 0.545:A:873:ALA:O 5:A:877:PRO:N 2.41 0.54
1:B:3586:MET:SD 1:B:3586:MET:N 2.81 0.546:F:0:PRO:HB3 7:G:371:HIS:HB3 1.90 0.548:E:365:GLU:O 8:E:368:TRP:HB2 2.08 0.546:F:428:LEU:CB 6:F:437:PHE:CE2 2.85 0.54
1:B:2635:GLN:NE2 1:B:3539:GLU:CB 2.70 0.543:D:168:UNK:O 3:D:170:UNK:N 2.41 0.54
6:F:438:ARG:HG2 6:F:440:LEU:HD22 1.90 0.541:B:2635:GLN:HE21 1:B:3539:GLU:CB 2.20 0.541:B:3100:LEU:O 1:B:3100:LEU:HD22 2.06 0.54
1:B:3247:ARG:HH12 1:B:3407:TYR:CB 2.21 0.546:F:35:PHE:CD1 6:F:36:PRO:HD2 2.43 0.54
1:B:3044:ALA:HB2 1:B:3060:TRP:CH2 2.43 0.533:D:424:UNK:O 3:D:428:UNK:N 2.42 0.536:F:66:ARG:HG3 6:F:69:TYR:CG 2.43 0.537:G:349:LEU:HD13 8:E:394:TYR:CD2 2.44 0.535:A:601:LEU:O 5:A:604:PHE:N 2.41 0.537:G:91:TYR:HA 7:G:95:ARG:HA 1.90 0.535:A:1044:LYS:C 5:A:1046:ALA:N 2.62 0.53
1:B:3062:PHE:CE2 1:B:3658:GLU:CB 2.91 0.531:B:3171:LEU:O 1:B:3172:ARG:C 2.47 0.531:B:3644:ASN:C 1:B:3647:THR:HG1 2.09 0.533:D:65:UNK:O 3:D:66:UNK:O 2.27 0.536:F:302:ALA:HA 6:F:306:ARG:HH21 1.73 0.536:F:447:GLU:HG2 6:F:450:TYR:OH 2.08 0.533:D:285:UNK:O 3:D:289:UNK:N 2.42 0.531:B:2961:ASP:O 1:B:2963:CYS:N 2.41 0.537:G:83:GLU:O 7:G:87:HIS:N 2.38 0.53
1:B:3568:THR:HG21 1:B:3739:ASN:HB3 1.91 0.532:C:694:TRP:HA 2:C:697:PHE:HD2 1.74 0.533:D:171:UNK:O 3:D:175:UNK:N 2.42 0.536:F:465:PHE:CE1 6:F:468:LEU:HD22 2.43 0.536:F:466:HIS:HA 6:F:469:TRP:CD1 2.44 0.535:A:2036:LEU:O 5:A:2039:GLU:N 2.42 0.535:A:1045:THR:CB 5:A:2511:VAL:CB 2.87 0.531:B:3099:GLU:HG2 1:B:3099:GLU:O 2.08 0.53
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Page 38 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3493:LEU:HD13 1:B:3497:HIS:HB2 1.89 0.532:C:677:THR:O 2:C:678:HIS:O 2.26 0.53
6:F:211:GLN:HB2 6:F:217:ILE:HB 1.90 0.536:F:444:HIS:C 6:F:446:ILE:N 2.52 0.536:F:84:ASP:O 6:F:87:GLN:HB3 2.08 0.535:A:1652:ILE:O 5:A:1654:ASN:N 2.41 0.53
1:B:3020:ALA:HB1 1:B:3050:ASP:CB 2.39 0.531:B:3354:ILE:CB 1:B:3355:PRO:HD2 2.38 0.533:D:170:UNK:O 3:D:174:UNK:N 2.42 0.535:A:410:GLU:O 5:A:412:GLU:N 2.42 0.531:B:2822:GLN:C 1:B:2824:SER:N 2.61 0.533:D:180:UNK:C 3:D:182:UNK:H 2.21 0.536:F:151:GLY:H 8:E:370:GLN:HE22 1.57 0.535:A:982:ILE:CB 5:A:2480:PHE:C 2.78 0.52
1:B:3107:LEU:HD12 1:B:3110:ILE:HD12 1.90 0.521:B:3389:ARG:O 1:B:3404:ALA:HA 2.10 0.521:B:3505:ASP:HA 1:B:3508:ILE:HB 1.91 0.526:F:249:ILE:HD12 6:F:420:LEU:HB2 1.91 0.521:B:3517:ILE:O 1:B:3520:MET:N 2.43 0.526:F:190:ILE:O 6:F:194:ILE:HG13 2.09 0.527:G:80:ASP:O 7:G:83:GLU:HB3 2.08 0.52
1:B:3246:PHE:HE2 1:B:3322:GLU:HA 1.75 0.522:C:689:GLU:C 2:C:691:ARG:H 2.12 0.521:B:2944:ALA:N 1:B:2970:ILE:CD1 2.73 0.52
1:B:3541:PHE:HE2 1:B:3545:ARG:NE 2.07 0.526:F:8:VAL:CG2 8:E:368:TRP:HB3 2.38 0.52
6:F:442:THR:HG1 6:F:443:GLY:H 1.52 0.521:B:3085:TYR:O 1:B:3104:ILE:CD1 2.56 0.521:B:3436:THR:O 1:B:3440:SER:N 2.43 0.526:F:19:ILE:HG22 6:F:21:PRO:HD3 1.91 0.526:F:80:VAL:HB 6:F:83:TRP:CH2 2.43 0.525:A:516:GLU:C 5:A:518:MET:N 2.62 0.521:B:3576:LYS:CD 1:B:3576:LYS:N 2.73 0.526:F:119:GLU:O 6:F:123:LYS:N 2.24 0.525:A:430:THR:O 5:A:432:GLN:CA 2.56 0.525:A:787:HIS:O 5:A:791:LEU:N 2.28 0.522:C:692:THR:N 2:C:693:PRO:CD 2.73 0.526:F:62:ILE:HG12 6:F:71:LEU:HD23 1.91 0.527:G:86:TRP:NE1 7:G:105:LEU:HD21 2.24 0.521:B:3160:ALA:HA 1:B:3167:LEU:CD2 2.39 0.521:B:3387:SER:O 1:B:3388:TYR:O 2.27 0.52
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Page 39 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3553:SER:O 1:B:3556:VAL:HG22 2.10 0.526:F:114:VAL:HG11 6:F:180:THR:HG21 1.92 0.526:F:442:THR:HG21 6:F:448:ARG:HG2 1.91 0.526:F:447:GLU:HG2 6:F:450:TYR:CZ 2.45 0.521:B:3432:LYS:NZ 1:B:3432:LYS:CB 2.73 0.521:B:3432:LYS:HZ2 1:B:3432:LYS:HB2 1.74 0.521:B:3721:LEU:HA 1:B:3724:ILE:HD12 1.91 0.522:C:722:GLN:O 2:C:724:LEU:N 2.42 0.526:F:151:GLY:H 8:E:370:GLN:NE2 2.07 0.52
7:G:169:PHE:CE1 8:E:381:VAL:HG22 2.45 0.525:A:1027:LEU:O 5:A:1030:LYS:N 2.37 0.51
1:B:3246:PHE:CE2 1:B:3322:GLU:HA 2.45 0.511:B:3706:LEU:CB 1:B:3720:ILE:HG13 2.40 0.516:F:291:GLU:HG3 6:F:296:LYS:H 1.75 0.517:G:208:ILE:HD12 7:G:208:ILE:H 1.75 0.513:D:438:UNK:O 6:F:266:ALA:N 2.42 0.515:A:389:PRO:O 5:A:390:LEU:C 2.48 0.51
1:B:2659:GLU:HG2 1:B:2681:ARG:CB 2.36 0.511:B:3020:ALA:CB 1:B:3050:ASP:CB 2.89 0.511:B:3418:ARG:NH1 1:B:3418:ARG:CG 2.73 0.511:B:3492:LYS:HD2 1:B:3492:LYS:H 1.75 0.511:B:3492:LYS:CD 1:B:3492:LYS:N 2.73 0.516:F:151:GLY:O 8:E:367:LYS:HE2 2.11 0.516:F:20:ASP:OD2 6:F:453:TRP:N 2.43 0.515:A:958:GLN:O 5:A:960:LEU:N 2.43 0.511:B:3551:GLN:O 1:B:3553:SER:N 2.43 0.512:C:739:SER:CA 3:D:328:UNK:O 2.58 0.513:D:414:UNK:C 3:D:416:UNK:H 2.22 0.515:A:1157:ILE:C 5:A:1159:GLU:N 2.60 0.515:A:348:LEU:O 5:A:352:ARG:N 2.36 0.511:B:2998:GLU:O 1:B:2999:LEU:C 2.48 0.515:A:2012:ASN:O 5:A:2016:PHE:N 2.43 0.516:F:48:THR:O 6:F:50:ASP:N 2.44 0.517:G:37:ARG:C 7:G:65:LEU:HB3 2.31 0.515:A:1103:LEU:O 5:A:1105:ASN:N 2.40 0.515:A:972:LEU:O 5:A:973:ASP:C 2.47 0.511:B:2898:TRP:C 1:B:2898:TRP:HE3 2.13 0.511:B:3171:LEU:O 1:B:3174:THR:CB 2.59 0.511:B:3464:PHE:HA 1:B:3576:LYS:NZ 2.26 0.511:B:3666:PHE:HA 1:B:3669:ASP:OD2 2.10 0.517:G:9:VAL:HG13 7:G:104:LEU:HD23 1.93 0.51
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Page 40 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
5:A:2541:PHE:O 5:A:2544:SER:N 2.44 0.515:A:957:ARG:O 5:A:959:PHE:N 2.44 0.51
1:B:3097:ILE:CD1 1:B:3097:ILE:N 2.73 0.511:B:3555:PHE:CD1 1:B:3581:VAL:HG11 2.45 0.516:F:241:GLU:HA 6:F:244:GLU:HG3 1.92 0.515:A:1867:LEU:O 5:A:1871:PHE:N 2.41 0.515:A:978:ALA:O 5:A:990:PRO:HA 2.11 0.51
1:B:3444:ASN:ND2 1:B:3580:ASN:HD22 2.08 0.511:B:3461:SER:CB 1:B:3464:PHE:CE2 2.94 0.511:B:3551:GLN:CD 1:B:3580:ASN:HA 2.31 0.511:B:3071:GLU:O 1:B:3072:PRO:C 2.48 0.511:B:3242:ASP:O 1:B:3245:LEU:N 2.44 0.511:B:3504:PRO:O 1:B:3507:THR:OG1 2.24 0.511:B:3576:LYS:HD3 1:B:3576:LYS:N 2.20 0.516:F:24:TYR:CD2 6:F:25:THR:HG23 2.46 0.507:G:109:PRO:HD2 7:G:161:HIS:CD2 2.46 0.507:G:132:PHE:CG 7:G:133:TYR:N 2.78 0.507:G:313:MET:O 7:G:317:ILE:HG12 2.11 0.505:A:137:LEU:C 5:A:139:SER:N 2.63 0.505:A:328:LEU:O 5:A:332:LEU:N 2.39 0.50
1:B:3247:ARG:CG 1:B:3248:LEU:N 2.74 0.501:B:3474:PHE:CD2 1:B:3526:VAL:CB 2.94 0.50
6:F:48:THR:C 6:F:50:ASP:H 2.14 0.505:A:871:VAL:O 5:A:874:PRO:N 2.45 0.501:B:2639:ILE:O 1:B:2643:ILE:N 2.43 0.501:B:3462:VAL:C 1:B:3464:PHE:N 2.65 0.506:F:27:ASN:ND2 6:F:450:TYR:HA 2.26 0.507:G:109:PRO:HG2 7:G:161:HIS:CD2 2.46 0.507:G:78:ASN:ND2 7:G:81:ASP:OD2 2.44 0.501:B:2633:TRP:CB 5:A:2625:TYR:N 2.75 0.505:A:425:GLU:O 5:A:426:SER:CB 2.60 0.501:B:2651:ASN:C 1:B:2653:LYS:N 2.64 0.506:F:187:GLY:O 6:F:243:LYS:NZ 2.44 0.505:A:1441:LEU:O 5:A:1445:PHE:CB 2.59 0.505:A:511:ASP:O 5:A:515:GLU:CA 2.60 0.505:A:1038:ASN:O 5:A:1039:TYR:C 2.50 0.501:B:2888:LEU:HA 5:A:953:GLY:HA2 1.94 0.505:A:982:ILE:CB 5:A:2481:ASN:N 2.75 0.50
1:B:3668:ARG:HG2 1:B:3672:ILE:HG23 1.93 0.507:G:138:ALA:C 7:G:165:ILE:CD1 2.80 0.50
7:G:208:ILE:HG12 7:G:243:PRO:HG3 1.92 0.50Continued on next page...
Page 41 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
5:A:2381:ALA:O 5:A:2384:ILE:CB 2.60 0.501:B:3068:LEU:HB2 1:B:3078:ALA:HB2 1.83 0.501:B:3574:VAL:HA 1:B:3580:ASN:O 2.12 0.501:B:3618:GLU:O 1:B:3620:VAL:CA 2.60 0.50
1:B:3106:TRP:HE3 1:B:3665:LEU:HD12 1.73 0.502:C:695:GLN:O 2:C:699:ARG:HG2 2.11 0.503:D:11:UNK:O 3:D:13:UNK:N 2.44 0.501:B:3171:LEU:O 1:B:3174:THR:CA 2.60 0.491:B:3474:PHE:C 1:B:3474:PHE:CD1 2.85 0.496:F:412:GLY:O 6:F:415:SER:OG 2.28 0.497:G:345:ILE:O 7:G:349:LEU:HG 2.12 0.495:A:2260:ALA:O 5:A:2261:TRP:C 2.50 0.497:G:155:SER:HA 7:G:160:THR:HG23 1.93 0.497:G:139:VAL:N 7:G:165:ILE:CD1 2.75 0.49
1:B:2737:ALA:CB 1:B:2746:LEU:HD11 2.42 0.491:B:2912:ILE:CD1 1:B:2912:ILE:N 2.74 0.496:F:128:LEU:HD13 6:F:134:PHE:CE2 2.48 0.496:F:182:ARG:N 6:F:388:LEU:HD11 2.26 0.49
7:G:275:ASP:OD2 7:G:316:GLU:HB3 2.12 0.497:G:360:GLN:O 7:G:364:GLU:N 2.45 0.49
2:C:690:ARG:HH12 2:C:763:ALA:HB1 1.78 0.497:G:125:GLU:HG3 7:G:362:TYR:OH 2.13 0.494:H:185:LEU:O 4:H:189:ARG:N 2.32 0.49
1:B:3040:ASN:OD1 1:B:3060:TRP:HZ2 1.93 0.491:B:3424:ARG:HG2 1:B:3424:ARG:NH2 2.27 0.496:F:148:PHE:CD2 6:F:459:LEU:HD11 2.47 0.497:G:10:ILE:HG12 7:G:19:ALA:HB1 1.94 0.497:G:312:ARG:O 7:G:316:GLU:HG2 2.12 0.495:A:736:PHE:N 5:A:1543:LEU:O 2.46 0.495:A:1652:ILE:C 5:A:1654:ASN:H 2.15 0.49
1:B:2944:ALA:CA 1:B:2970:ILE:CD1 2.88 0.491:B:3570:HIS:C 1:B:3570:HIS:CD2 2.85 0.496:F:58:SER:HB2 6:F:92:TRP:CH2 2.47 0.497:G:138:ALA:HB1 7:G:163:VAL:HG12 1.95 0.497:G:286:ASP:HB2 7:G:288:ASP:OD1 2.11 0.495:A:1745:LEU:O 5:A:1749:ASP:N 2.32 0.491:B:3393:ILE:CB 1:B:3400:VAL:HA 2.43 0.491:B:3407:TYR:N 1:B:3408:PRO:HD3 2.20 0.491:B:3450:PRO:C 1:B:3451:LEU:HD13 2.27 0.493:D:3:UNK:O 3:D:7:UNK:N 2.45 0.49
6:F:122:LYS:HG2 6:F:484:LEU:HD11 1.94 0.49Continued on next page...
Page 42 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
6:F:72:LYS:CD 6:F:73:PRO:HD2 2.41 0.495:A:741:LEU:O 5:A:744:LEU:N 2.46 0.491:B:2670:GLN:O 1:B:2837:PRO:HB3 2.11 0.49
1:B:3474:PHE:CE2 1:B:3526:VAL:CB 2.88 0.492:C:697:PHE:CD1 2:C:697:PHE:C 2.85 0.496:F:118:THR:HA 6:F:121:ARG:HD2 1.95 0.496:F:132:MET:HB2 6:F:134:PHE:CZ 2.47 0.496:F:193:LEU:HD21 6:F:299:ASP:HB3 1.95 0.495:A:2169:TYR:O 5:A:2173:LYS:N 2.46 0.495:A:2539:SER:O 5:A:2543:ASP:N 2.30 0.495:A:806:LEU:O 5:A:809:PHE:N 2.46 0.49
7:G:349:LEU:HD13 8:E:394:TYR:CE2 2.48 0.496:F:205:PRO:HG3 6:F:230:TYR:CD1 2.48 0.491:B:3086:LEU:HA 1:B:3104:ILE:HD12 1.94 0.481:B:3246:PHE:C 1:B:3246:PHE:CD1 2.85 0.481:B:3559:SER:HG 1:B:3560:TYR:N 2.11 0.486:F:70:GLU:HB2 6:F:226:ASP:OD2 2.11 0.486:F:466:HIS:HA 6:F:469:TRP:HD1 1.76 0.487:G:139:VAL:CA 7:G:165:ILE:HD13 2.43 0.481:B:3697:ASP:O 1:B:3701:ARG:HG3 2.13 0.483:D:215:UNK:O 3:D:216:UNK:CB 2.59 0.481:B:3143:SER:OG 1:B:3204:PRO:CB 2.61 0.482:C:763:ALA:O 2:C:767:CYS:N 2.42 0.486:F:297:GLU:O 6:F:300:ILE:N 2.44 0.485:A:1012:HIS:C 5:A:1014:ARG:N 2.67 0.481:B:3040:ASN:O 1:B:3060:TRP:HZ2 1.95 0.481:B:3098:ARG:O 1:B:3134:ILE:CB 2.61 0.481:B:3360:LEU:CB 1:B:3424:ARG:HH22 2.18 0.481:B:3372:ALA:HB3 1:B:3395:GLY:HA2 1.95 0.481:B:3503:ALA:O 1:B:3506:MET:HB3 2.13 0.48
1:B:3674:TRP:CZ3 1:B:3678:LEU:HB2 2.48 0.486:F:145:CYS:O 6:F:455:GLY:HA3 2.14 0.485:A:1962:THR:O 5:A:1966:TRP:N 2.31 0.481:B:3068:LEU:CB 1:B:3078:ALA:HA 2.40 0.481:B:3649:SER:HB2 1:B:3704:ALA:C 2.33 0.487:G:124:PHE:HB2 7:G:362:TYR:CD2 2.48 0.487:G:336:LYS:HG2 7:G:337:TYR:CE1 2.48 0.485:A:1012:HIS:C 5:A:1014:ARG:H 2.15 0.48
1:B:3468:HIS:ND1 1:B:3569:PRO:HB2 2.28 0.487:G:101:HIS:O 7:G:103:VAL:HG23 2.13 0.487:G:310:ALA:O 7:G:313:MET:HB2 2.14 0.48
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Page 43 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:2791:ARG:O 1:B:2792:GLN:C 2.51 0.481:B:3236:ARG:NE 1:B:3338:CYS:CB 2.76 0.481:B:3646:PHE:CB 1:B:3720:ILE:CD1 2.92 0.488:E:357:THR:N 8:E:361:ILE:HD12 2.29 0.487:G:312:ARG:O 7:G:316:GLU:N 2.28 0.481:B:3062:PHE:HZ 1:B:3658:GLU:HA 1.77 0.481:B:3650:ARG:O 1:B:3654:GLU:N 2.45 0.487:G:190:MET:SD 7:G:203:THR:HG22 2.53 0.481:B:2663:LEU:HA 1:B:2663:LEU:HD13 1.72 0.48
1:B:3509:LEU:HD12 1:B:3510:LYS:N 2.28 0.483:D:162:UNK:O 3:D:165:UNK:N 2.47 0.483:D:2:UNK:CB 3:D:16:UNK:HA 2.44 0.486:F:118:THR:O 6:F:121:ARG:HB2 2.13 0.485:A:2257:VAL:O 5:A:2261:TRP:N 2.41 0.476:F:190:ILE:HD11 6:F:292:LEU:HD11 1.96 0.476:F:444:HIS:O 6:F:447:GLU:N 2.47 0.47
6:F:447:GLU:HA 6:F:450:TYR:CE1 2.49 0.477:G:371:HIS:O 8:E:380:LYS:NZ 2.33 0.47
7:G:355:MET:HA 7:G:373:LYS:HZ1 1.80 0.475:A:1560:HIS:CB 5:A:1598:ARG:CB 2.92 0.475:A:1646:ASN:O 5:A:1648:TYR:N 2.47 0.47
1:B:2748:GLU:HB3 1:B:2752:HIS:NE2 2.29 0.477:G:261:LEU:HB3 7:G:274:ILE:HD13 1.96 0.475:A:834:ILE:O 5:A:838:LEU:N 2.27 0.471:B:3085:TYR:C 1:B:3104:ILE:HD13 2.24 0.473:D:168:UNK:O 3:D:169:UNK:C 2.62 0.476:F:213:LYS:CB 6:F:214:PRO:HD3 2.35 0.476:F:241:GLU:O 6:F:244:GLU:HB2 2.14 0.47
6:F:244:GLU:HB3 7:G:287:VAL:CG1 2.44 0.475:A:982:ILE:CB 5:A:2481:ASN:HA 2.42 0.47
1:B:3449:ILE:HG22 1:B:3451:LEU:HD11 1.97 0.472:C:695:GLN:O 2:C:699:ARG:CD 2.61 0.47
2:C:702:GLN:OE1 2:C:702:GLN:HA 2.14 0.476:F:432:LEU:HD21 6:F:435:LEU:HD22 1.96 0.476:F:36:PRO:HB3 6:F:453:TRP:CE2 2.48 0.476:F:174:MET:HA 6:F:489[A]:ARG:HB3 1.95 0.477:G:124:PHE:HB2 7:G:362:TYR:CE2 2.49 0.477:G:72:GLU:HB2 7:G:77:THR:HG21 1.97 0.471:B:2898:TRP:C 1:B:2898:TRP:CE3 2.88 0.471:B:2941:HIS:C 1:B:2943:ILE:H 2.18 0.47
1:B:3427:ASN:CA 1:B:3443:PHE:HZ 2.17 0.47Continued on next page...
Page 44 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3427:ASN:HD22 1:B:3428:LYS:H 1.61 0.476:F:107:PRO:HB2 6:F:469:TRP:CH2 2.49 0.475:A:1091:SER:HA 5:A:1099:ALA:CA 2.44 0.475:A:1417:LYS:HA 5:A:1420:ALA:HB3 1.97 0.475:A:1581:GLU:O 5:A:1585:ARG:CB 2.63 0.471:B:3491:ASP:HB3 1:B:3492:LYS:NZ 2.30 0.471:B:3545:ARG:NH1 1:B:3633:GLY:HA2 2.29 0.47
8:E:392:LYS:O 8:E:396:THR:HG23 2.15 0.477:G:351:THR:O 7:G:354:GLN:HG2 2.15 0.475:A:2352:ILE:O 5:A:2356:SER:N 2.46 0.471:B:2637:ILE:HA 1:B:2640:LEU:HB3 1.95 0.471:B:2839:HIS:O 1:B:2843:LEU:HG 2.15 0.471:B:3481:ASP:CB 1:B:3482:PRO:HD3 2.42 0.471:B:3658:GLU:O 1:B:3662:TYR:N 2.38 0.47
6:F:442:THR:HG21 6:F:448:ARG:HG3 1.92 0.475:A:1086:VAL:O 5:A:1090:THR:N 2.38 0.475:A:461:LYS:O 5:A:465:MET:N 2.32 0.471:B:3699:ILE:O 1:B:3702:LYS:N 2.48 0.47
1:B:3721:LEU:HG 1:B:3724:ILE:HD12 1.96 0.477:G:9:VAL:O 7:G:20:GLY:N 2.48 0.47
5:A:1201:CYS:C 5:A:1203:ASP:H 2.18 0.471:B:3065:ASP:O 1:B:3068:LEU:HG 2.14 0.47
1:B:3493:LEU:HD13 1:B:3493:LEU:O 2.14 0.473:D:4:UNK:O 3:D:8:UNK:N 2.47 0.474:H:86:ASN:O 4:H:89:PRO:N 2.47 0.47
1:B:2969:ARG:O 1:B:2969:ARG:HD3 2.15 0.471:B:3100:LEU:HD13 1:B:3101:LEU:HA 1.97 0.471:B:3731:ARG:HB3 2:C:694:TRP:HE1 1.80 0.473:D:420:UNK:C 3:D:422:UNK:N 2.77 0.47
7:G:180:LEU:HD23 7:G:184:ASP:OD2 2.14 0.477:G:359:LYS:O 7:G:362:TYR:HB3 2.15 0.475:A:31:LEU:O 5:A:35:MET:N 2.48 0.475:A:330:ILE:O 5:A:334:GLN:CB 2.63 0.47
1:B:3163:TYR:CB 1:B:3167:LEU:HB3 2.45 0.478:E:391:ILE:CA 8:E:394:TYR:HB2 2.32 0.475:A:1043:LEU:O 5:A:1046:ALA:N 2.46 0.461:B:2837:PRO:O 1:B:2840:LYS:N 2.47 0.461:B:3366:VAL:O 1:B:3367:HIS:C 2.51 0.46
1:B:3649:SER:HB2 1:B:3705:GLN:CA 2.42 0.461:B:3668:ARG:NE 1:B:3672:ILE:HD13 2.15 0.466:F:264:SER:O 6:F:265:THR:OG1 2.30 0.46
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Page 45 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
7:G:82:MET:HG3 7:G:86:TRP:CZ2 2.50 0.465:A:1036:PRO:O 5:A:1039:TYR:N 2.33 0.465:A:1345:LEU:CA 5:A:1349:MET:CB 2.92 0.465:A:2092:LEU:O 5:A:2095:ALA:HB3 2.14 0.461:B:3244:ASP:O 1:B:3247:ARG:CD 2.63 0.461:B:3740:PHE:CB 1:B:3742:PRO:CD 2.84 0.463:D:61:UNK:C 3:D:63:UNK:N 2.78 0.467:G:255:PHE:C 7:G:258:PRO:HD2 2.35 0.461:B:2651:ASN:N 1:B:2651:ASN:ND2 2.60 0.461:B:3668:ARG:NE 1:B:3672:ILE:HG21 2.29 0.461:B:3496:ALA:CB 2:C:684:TYR:CD1 2.98 0.466:F:152:ARG:HD3 6:F:407:ASN:OD1 2.15 0.465:A:1581:GLU:C 5:A:1583:LYS:H 2.17 0.465:A:981:LYS:CB 5:A:988:ASP:HA 2.44 0.464:H:183:LYS:O 4:H:186:LYS:N 2.49 0.465:A:1003:ILE:CB 5:A:1017:ALA:HB2 2.45 0.465:A:1948:VAL:O 5:A:1952:VAL:N 2.31 0.461:B:3427:ASN:N 1:B:3443:PHE:HZ 2.09 0.461:B:3464:PHE:HA 1:B:3576:LYS:HZ1 1.81 0.466:F:110:LEU:HD23 6:F:111:THR:N 2.31 0.466:F:285:ARG:HA 6:F:288:PHE:CE2 2.50 0.466:F:72:LYS:CB 6:F:72:LYS:NZ 2.73 0.467:G:14:SER:HB2 7:G:157:ASP:CB 2.45 0.467:G:286:ASP:HB2 7:G:288:ASP:CG 2.35 0.465:A:1102:LEU:O 5:A:1106:LEU:N 2.38 0.46
1:B:3107:LEU:HD12 1:B:3110:ILE:CD1 2.45 0.468:E:358:HIS:CG 8:E:359:GLN:H 2.34 0.463:D:139:UNK:O 6:F:178:LYS:HE3 2.16 0.46
6:F:241:GLU:HG3 6:F:244:GLU:OE1 2.15 0.467:G:101:HIS:O 7:G:130:PRO:HD2 2.15 0.463:D:102:UNK:C 3:D:233:UNK:HA 2.45 0.466:F:47:TYR:CD1 6:F:50:ASP:OD2 2.68 0.466:F:95:GLN:O 6:F:99:TYR:HA 2.16 0.46
7:G:277:THR:HA 7:G:280:ASN:HD22 1.81 0.467:G:286:ASP:O 7:G:290:ARG:NE 2.49 0.465:A:1868:SER:O 5:A:1872:ILE:N 2.48 0.46
1:B:2737:ALA:HB3 1:B:2746:LEU:HD11 1.98 0.461:B:3082:ILE:CB 1:B:3108:ILE:HD11 2.46 0.466:F:43:VAL:HG22 6:F:73:PRO:HA 1.97 0.465:A:1589:ASP:O 5:A:1590:SER:C 2.54 0.465:A:914:ASP:O 5:A:916:ILE:N 2.47 0.46
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Page 46 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3242:ASP:O 1:B:3243:GLU:C 2.52 0.466:F:390:TYR:HD1 6:F:432:LEU:HD12 1.80 0.466:F:444:HIS:CE1 8:E:377:HIS:HE1 2.34 0.465:A:1041:GLU:HA 5:A:2514:VAL:CB 2.46 0.465:A:709:VAL:O 5:A:713:MET:N 2.49 0.46
1:B:3505:ASP:HA 1:B:3508:ILE:HD12 1.97 0.468:E:378:LYS:O 8:E:382:ALA:N 2.42 0.46
7:G:162:VAL:HG11 7:G:278:THR:HA 1.98 0.467:G:33:SER:CB 7:G:71:ILE:HG13 2.46 0.465:A:2334:SER:O 5:A:2338:LEU:N 2.42 0.451:B:2639:ILE:HA 1:B:2642:SER:HB3 1.98 0.451:B:3404:ALA:CA 1:B:3457:ILE:HG22 2.46 0.451:B:3555:PHE:CE1 1:B:3581:VAL:HG11 2.51 0.452:C:699:ARG:CD 2:C:699:ARG:N 2.73 0.457:G:180:LEU:HD21 7:G:269:LEU:HD21 1.97 0.457:G:140:LEU:HD11 7:G:343:GLY:CA 2.45 0.451:B:3068:LEU:CB 1:B:3078:ALA:CA 2.94 0.451:B:2957:HIS:HA 1:B:3434:VAL:CB 2.46 0.451:B:3496:ALA:HB3 1:B:3510:LYS:HZ2 1.81 0.457:G:108:ALA:HB1 7:G:109:PRO:HD3 1.96 0.457:G:309:ILE:O 7:G:313:MET:HG2 2.16 0.457:G:99:GLU:C 7:G:130:PRO:HD3 2.37 0.451:B:2675:PHE:O 1:B:2675:PHE:CG 2.69 0.456:F:10:GLY:C 6:F:12:ASP:H 2.19 0.456:F:443:GLY:O 6:F:444:HIS:HD2 1.99 0.457:G:273:GLY:N 7:G:276:GLN:HB3 2.31 0.456:F:122:LYS:HA 6:F:125:LEU:HD12 1.98 0.457:G:360:GLN:O 7:G:364:GLU:HG3 2.17 0.455:A:1091:SER:CA 5:A:1099:ALA:CA 2.90 0.455:A:967:THR:O 5:A:968:GLU:C 2.55 0.451:B:3060:TRP:O 1:B:3061:GLY:C 2.53 0.45
6:F:156:LEU:HD12 6:F:168:SER:O 2.17 0.457:G:24:ASP:HB2 7:G:340:TRP:CH2 2.46 0.451:B:3731:ARG:CB 2:C:694:TRP:HE1 2.29 0.455:A:1207:TYR:O 5:A:1208:ASN:C 2.55 0.451:B:3096:LYS:C 1:B:3097:ILE:HD13 2.35 0.45
1:B:3236:ARG:HD2 1:B:3236:ARG:HA 1.48 0.451:B:3296:PHE:O 1:B:3296:PHE:CD1 2.70 0.451:B:3437:ARG:O 1:B:3439:ARG:N 2.50 0.451:B:3555:PHE:CZ 1:B:3583:THR:HG21 2.52 0.453:D:310:UNK:O 3:D:313:UNK:N 2.49 0.45
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Page 47 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
6:F:272:SER:HB3 6:F:278:ILE:HG12 1.99 0.456:F:291:GLU:OE2 6:F:296:LYS:HB2 2.17 0.455:A:580:ILE:C 5:A:583:ALA:H 2.19 0.451:B:2874:ALA:C 1:B:2876:GLU:H 2.18 0.451:B:3467:LEU:C 1:B:3467:LEU:CD1 2.86 0.451:B:3699:ILE:O 1:B:3700:ILE:C 2.55 0.458:E:366:ALA:C 8:E:368:TRP:N 2.70 0.457:G:143:TYR:CG 8:E:391:ILE:HG21 2.51 0.456:F:216:PHE:CE2 6:F:218:LYS:HG3 2.52 0.457:G:124:PHE:HD1 7:G:359:LYS:HG2 1.82 0.455:A:1650:PHE:C 5:A:1652:ILE:N 2.70 0.455:A:1673:PHE:O 5:A:1676:MET:N 2.50 0.455:A:239:LYS:O 5:A:240:GLN:C 2.47 0.45
1:B:3424:ARG:HH21 1:B:3424:ARG:CG 2.30 0.451:B:3474:PHE:CE2 1:B:3526:VAL:CG1 2.92 0.452:C:704:ASN:CB 2:C:711:ASP:HA 2.46 0.453:D:420:UNK:O 3:D:422:UNK:N 2.50 0.456:F:406:HIS:CD2 6:F:406:HIS:O 2.70 0.456:F:175:THR:N 6:F:489[B]:ARG:HG2 2.31 0.457:G:148:THR:HB 8:E:388:ALA:HB1 1.99 0.457:G:138:ALA:CA 7:G:152:VAL:HG11 2.40 0.457:G:346:LEU:HG 7:G:352:PHE:CE2 2.52 0.455:A:592:SER:O 5:A:596:THR:N 2.38 0.451:B:2885:ARG:C 1:B:2885:ARG:CD 2.85 0.45
7:G:216:LEU:HD22 7:G:238:LYS:HD2 1.99 0.457:G:271:SER:OG 7:G:272:ALA:N 2.50 0.451:B:2821:ILE:HA 1:B:2849:TYR:CZ 2.52 0.441:B:3015:GLY:C 1:B:3019:LYS:HB3 2.38 0.441:B:3159:ILE:O 1:B:3163:TYR:CB 2.65 0.441:B:3358:TYR:O 1:B:3358:TYR:CG 2.70 0.44
1:B:3100:LEU:HD13 1:B:3101:LEU:H 1.67 0.441:B:3316:TYR:CD1 1:B:3316:TYR:O 2.70 0.441:B:3592:PRO:CB 1:B:3671:ILE:HB 2.47 0.441:B:3649:SER:CB 1:B:3705:GLN:CA 2.82 0.443:D:373:UNK:H 8:E:379:TYR:HE1 1.57 0.443:D:38:UNK:O 3:D:39:UNK:C 2.65 0.44
6:F:253:LYS:HB3 6:F:256:GLU:HG2 1.98 0.446:F:204:ILE:HD12 6:F:274:TRP:CD2 2.52 0.44
7:G:73:HIS:N 7:G:73:HIS:ND1 2.64 0.447:G:81:ASP:O 7:G:84:LYS:N 2.51 0.445:A:119:MET:O 5:A:123:THR:N 2.46 0.44
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Page 48 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
5:A:302:THR:C 5:A:304:PHE:N 2.71 0.441:B:2874:ALA:C 1:B:2876:GLU:N 2.71 0.44
1:B:2898:TRP:CE3 1:B:2898:TRP:O 2.70 0.443:D:384:UNK:O 3:D:386:UNK:N 2.50 0.44
6:F:127:VAL:HG12 6:F:128:LEU:HD23 1.99 0.441:B:2844:HIS:C 1:B:2846:PHE:N 2.70 0.441:B:3504:PRO:O 1:B:3508:ILE:HG13 2.18 0.441:B:3617:ASN:O 1:B:3618:GLU:C 2.55 0.446:F:475:TYR:CD1 6:F:475:TYR:C 2.85 0.445:A:2549:PHE:HZ 5:A:2556:ILE:HA 1.82 0.44
1:B:2651:ASN:HD22 1:B:2651:ASN:N 2.13 0.441:B:3439:ARG:HG3 1:B:3441:ILE:HG12 2.00 0.441:B:3424:ARG:HH11 1:B:3447:ILE:HA 1.65 0.44
1:B:3570:HIS:O 1:B:3570:HIS:CG 2.70 0.446:F:258:THR:HA 6:F:261:GLU:HG2 1.99 0.447:G:187:ASP:OD1 7:G:206:ARG:NH1 2.51 0.447:G:210:ARG:O 7:G:213:LYS:HB3 2.17 0.444:H:183:LYS:O 4:H:184:LEU:C 2.56 0.445:A:1207:TYR:O 5:A:1210:ARG:N 2.51 0.44
1:B:3172:ARG:NH2 1:B:3173:THR:HA 2.32 0.441:B:3106:TRP:CB 1:B:3665:LEU:CD1 2.81 0.446:F:400:LEU:O 6:F:404:LEU:HG 2.18 0.446:F:57:PHE:CE1 6:F:89:GLN:HB2 2.53 0.447:G:230:ALA:CB 7:G:252:ASN:HB3 2.47 0.447:G:117:GLU:HG2 7:G:367:PRO:O 2.17 0.445:A:1605:ASN:C 5:A:1607:VAL:N 2.71 0.445:A:1859:LEU:C 5:A:1861:ARG:H 2.20 0.442:C:688:ILE:HA 2:C:691:ARG:HE 1.82 0.446:F:18:VAL:O 6:F:28:ILE:HG23 2.18 0.446:F:406:HIS:CG 6:F:406:HIS:O 2.70 0.447:G:16:MET:H 7:G:16:MET:HE1 1.74 0.447:G:24:ASP:HB3 7:G:26:ALA:H 1.83 0.441:B:2675:PHE:O 1:B:2675:PHE:CD1 2.71 0.441:B:2843:LEU:O 1:B:2846:PHE:N 2.39 0.442:C:732:GLN:O 2:C:734:GLN:N 2.50 0.445:A:2389:SER:O 5:A:2391:SER:N 2.50 0.44
1:B:3068:LEU:HD12 1:B:3068:LEU:C 2.39 0.441:B:3358:TYR:O 1:B:3358:TYR:CD2 2.71 0.44
1:B:3247:ARG:HH11 1:B:3407:TYR:CB 2.29 0.442:C:691:ARG:HG3 2:C:692:THR:N 2.33 0.448:E:364:GLU:O 8:E:368:TRP:HD1 2.01 0.44
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Page 49 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
6:F:186:ALA:O 6:F:189:PHE:N 2.49 0.446:F:484:LEU:HA 6:F:487:ARG:HH11 1.82 0.447:G:35:VAL:N 7:G:68:ARG:O 2.43 0.44
5:A:1038:ASN:O 5:A:1041:GLU:N 2.52 0.435:A:1653:SER:O 5:A:1654:ASN:C 2.56 0.431:B:3015:GLY:CA 1:B:3019:LYS:HB3 2.48 0.431:B:3570:HIS:O 1:B:3570:HIS:CD2 2.70 0.438:E:375:GLU:O 8:E:378:LYS:N 2.51 0.436:F:267:LYS:HA 6:F:282:ASN:HD21 1.83 0.435:A:2243:ILE:CB 5:A:2252:SER:CA 2.94 0.436:F:390:TYR:CD1 6:F:432:LEU:HD12 2.53 0.437:G:257:ALA:HB3 7:G:258:PRO:HD3 2.00 0.434:H:193:LEU:O 4:H:196:LEU:N 2.46 0.435:A:838:LEU:O 5:A:842:LEU:N 2.49 0.431:B:3552:TYR:O 1:B:3552:TYR:CD1 2.70 0.432:C:712:LEU:O 2:C:716:ARG:CB 2.66 0.43
7:G:253:GLU:HG2 7:G:256:ARG:HD3 2.00 0.437:G:326:LYS:HE3 7:G:328:LYS:HD2 2.01 0.431:B:3070:GLU:OE1 1:B:3070:GLU:HA 2.18 0.431:B:3451:LEU:CD1 1:B:3451:LEU:N 2.73 0.432:C:670:GLU:O 2:C:674:ALA:N 2.37 0.433:D:150:UNK:O 3:D:152:UNK:N 2.51 0.436:F:177:SER:HA 6:F:180:THR:HG23 2.00 0.436:F:244:GLU:HB3 7:G:287:VAL:HG11 1.99 0.437:G:130:PRO:HA 7:G:359:LYS:HZ3 1.83 0.437:G:140:LEU:CD1 7:G:343:GLY:CA 2.96 0.437:G:18:LYS:HE3 7:G:337:TYR:CD1 2.53 0.435:A:1044:LYS:O 5:A:1046:ALA:N 2.52 0.435:A:1044:LYS:C 5:A:1046:ALA:H 2.22 0.435:A:1255:ALA:O 5:A:1256:ILE:C 2.56 0.431:B:3085:TYR:CB 1:B:3104:ILE:HD13 2.48 0.431:B:3253:LEU:CD1 1:B:3318:ARG:HB2 2.45 0.431:B:3411:ARG:O 1:B:3415:ARG:CB 2.66 0.431:B:3546:LYS:NZ 1:B:3550:SER:HB2 2.34 0.432:C:649:ILE:O 2:C:652:SER:N 2.51 0.433:D:79:UNK:C 3:D:80:UNK:O 2.59 0.436:F:82:ASP:OD2 6:F:85:THR:OG1 2.34 0.437:G:137:GLN:HG3 7:G:339:VAL:CG1 2.48 0.437:G:223:PHE:HD1 7:G:259:GLU:HG3 1.84 0.435:A:2526:HIS:O 5:A:2530:MET:N 2.51 0.433:D:11:UNK:C 3:D:13:UNK:N 2.82 0.43
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Page 50 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
8:E:377:HIS:O 8:E:381:VAL:HG23 2.19 0.436:F:180:THR:O 6:F:181:ARG:NH1 2.42 0.43
1:B:2898:TRP:CZ3 1:B:2902:VAL:HG21 2.53 0.431:B:3108:ILE:HA 1:B:3108:ILE:HD12 1.74 0.431:B:3443:PHE:N 1:B:3443:PHE:CD1 2.73 0.43
1:B:3733:LEU:HD21 1:B:3742:PRO:HG2 2.00 0.436:F:94:LEU:O 6:F:99:TYR:N 2.52 0.43
7:G:253:GLU:HA 7:G:256:ARG:HB2 2.00 0.431:B:3488:PHE:CE1 1:B:3492:LYS:HG2 2.54 0.431:B:3493:LEU:CD1 1:B:3493:LEU:C 2.86 0.432:C:679:ARG:C 2:C:681:THR:H 2.22 0.43
6:F:413:GLY:HA3 6:F:449:GLN:NE2 2.33 0.436:F:48:THR:C 6:F:50:ASP:N 2.71 0.43
7:G:107:GLU:HB2 7:G:111:ASN:ND2 2.32 0.435:A:1988:PHE:O 5:A:1991:SER:N 2.42 0.435:A:2168:LEU:O 5:A:2172:PHE:N 2.49 0.431:B:3668:ARG:O 1:B:3671:ILE:HG13 2.18 0.436:F:128:LEU:HD13 6:F:134:PHE:CD2 2.53 0.436:F:302:ALA:C 6:F:304:TRP:H 2.22 0.436:F:416:SER:HA 6:F:448:ARG:NH1 2.34 0.436:F:462:LEU:HA 6:F:462:LEU:HD23 1.84 0.435:A:1417:LYS:O 5:A:1421:ILE:N 2.51 0.43
5:A:1986:TYR:HA 5:A:1989:LEU:CB 2.49 0.431:B:2898:TRP:HE3 1:B:2898:TRP:O 2.00 0.431:B:2947:ILE:CB 1:B:2970:ILE:HD12 2.49 0.431:B:3394:ARG:CA 1:B:3398:GLY:HA2 2.49 0.436:F:440:LEU:HD13 6:F:440:LEU:HA 1.75 0.437:G:116:ARG:HG2 7:G:370:VAL:HG21 2.01 0.435:A:21:LEU:O 5:A:25:TYR:N 2.44 0.42
1:B:3062:PHE:CZ 1:B:3658:GLU:HA 2.50 0.426:F:116:ASN:OD1 6:F:120:ASN:HB2 2.19 0.426:F:40:LEU:HB3 6:F:89:GLN:HE21 1.84 0.427:G:103:VAL:O 7:G:132:PHE:HD1 2.02 0.427:G:151:ILE:CG2 7:G:297:ILE:CG1 2.95 0.426:F:10:GLY:HA2 6:F:463:GLY:N 2.34 0.426:F:272:SER:HB3 6:F:278:ILE:CG1 2.49 0.421:B:2966:GLN:HA 1:B:2966:GLN:OE1 2.19 0.421:B:3493:LEU:CD1 1:B:3497:HIS:HB2 2.49 0.427:G:70:PRO:HG2 7:G:85:ILE:HD11 2.01 0.421:B:2844:HIS:HA 1:B:2847:GLN:CB 2.47 0.421:B:3168:HIS:ND1 1:B:3168:HIS:C 2.73 0.42
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Page 51 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3296:PHE:C 1:B:3296:PHE:CD1 2.92 0.421:B:3667:ILE:HG21 1:B:3696:VAL:CB 2.49 0.426:F:56:ILE:HD12 6:F:56:ILE:HA 1.68 0.426:F:87:GLN:O 6:F:132:MET:HE1 2.11 0.42
7:G:105:LEU:HD13 7:G:132:PHE:CE1 2.54 0.427:G:255:PHE:O 7:G:259:GLU:HG2 2.19 0.425:A:1249:GLN:C 5:A:1251:GLU:H 2.14 0.425:A:1581:GLU:O 5:A:1585:ARG:N 2.53 0.425:A:369:TYR:O 5:A:372:ASP:N 2.52 0.421:B:2648:SER:O 1:B:2649:ILE:CB 2.68 0.426:F:238:PHE:HZ 6:F:278:ILE:HG21 1.85 0.427:G:102:PRO:HA 7:G:131:ALA:O 2.20 0.426:F:2:SER:HB2 7:G:371:HIS:O 2.19 0.421:B:2761:GLU:O 1:B:2765:ARG:N 2.52 0.421:B:3163:TYR:CB 1:B:3167:LEU:CB 2.98 0.421:B:3247:ARG:O 1:B:3251:VAL:HG23 2.18 0.421:B:3418:ARG:HA 1:B:3418:ARG:HD3 1.26 0.421:B:3462:VAL:O 1:B:3464:PHE:CG 2.72 0.422:C:691:ARG:O 2:C:695:GLN:HG3 2.20 0.424:H:223:ASP:O 4:H:227:GLU:N 2.44 0.425:A:1345:LEU:O 5:A:1349:MET:CB 2.67 0.421:B:2635:GLN:N 1:B:2635:GLN:CD 2.72 0.42
1:B:2885:ARG:HD3 1:B:2886:ASP:N 2.34 0.421:B:3512:GLU:O 1:B:3515:ASN:HB3 2.19 0.421:B:3724:ILE:O 1:B:3727:ALA:N 2.50 0.422:C:649:ILE:O 2:C:653:GLU:N 2.49 0.423:D:424:UNK:O 3:D:425:UNK:C 2.67 0.426:F:175:THR:O 6:F:489[B]:ARG:NH2 2.48 0.426:F:243:LYS:HG2 6:F:247:CYS:SG 2.59 0.426:F:287:GLY:HA2 6:F:290:GLU:HB3 2.01 0.426:F:437:PHE:N 6:F:437:PHE:CD1 2.86 0.427:G:174:ALA:O 7:G:281:SER:OG 2.34 0.42
7:G:230:ALA:HB2 7:G:252:ASN:HB3 2.02 0.426:F:484:LEU:O 6:F:487:ARG:HG2 2.19 0.426:F:62:ILE:HG12 6:F:71:LEU:CD2 2.49 0.427:G:355:MET:HA 7:G:373:LYS:NZ 2.34 0.424:H:186:LYS:O 4:H:190:ASP:N 2.51 0.42
1:B:3101:LEU:CD1 1:B:3101:LEU:C 2.86 0.421:B:3360:LEU:CB 1:B:3424:ARG:HG2 2.50 0.426:F:19:ILE:HA 6:F:28:ILE:HG12 2.02 0.426:F:213:LYS:CE 6:F:213:LYS:CA 2.86 0.42
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Page 52 Full wwPDB EM Validation Report EMD-6816, 5Y81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
5:A:2180:ILE:O 5:A:2184:LEU:N 2.52 0.421:B:3106:TRP:CH2 1:B:3668:ARG:CZ 3.00 0.421:B:3492:LYS:O 1:B:3510:LYS:HE2 2.20 0.426:F:30:TYR:HB2 7:G:113:LYS:HE3 2.02 0.423:D:396:UNK:CA 6:F:436:LYS:HE3 2.48 0.427:G:133:TYR:CZ 7:G:374:CYS:HA 2.54 0.421:B:2778:GLN:O 1:B:2782:SER:N 2.30 0.411:B:3719:PHE:HA 1:B:3722:ASP:CB 2.49 0.411:B:3720:ILE:O 1:B:3723:CYS:N 2.52 0.41
6:F:164:THR:HG22 6:F:184:PHE:CD1 2.54 0.417:G:109:PRO:CD 7:G:161:HIS:CD2 3.03 0.417:G:163:VAL:HA 7:G:164:PRO:HD3 1.65 0.415:A:1300:ASN:C 5:A:1302:LYS:N 2.56 0.411:B:3229:LEU:C 1:B:3229:LEU:CD1 2.85 0.411:B:3354:ILE:CA 1:B:3371:ILE:H 2.22 0.411:B:3540:ASP:HA 1:B:3543:LEU:HD13 2.02 0.416:F:151:GLY:N 8:E:370:GLN:OE1 2.53 0.416:F:213:LYS:CG 6:F:214:PRO:HD3 2.50 0.417:G:151:ILE:HD12 7:G:152:VAL:N 2.36 0.417:G:180:LEU:HD21 7:G:269:LEU:HD11 2.01 0.417:G:149:THR:HG21 7:G:292:GLU:OE1 2.19 0.415:A:1673:PHE:O 5:A:1674:ASN:C 2.58 0.415:A:580:ILE:HA 5:A:583:ALA:HB3 2.01 0.412:C:694:TRP:HA 2:C:697:PHE:CD2 2.53 0.418:E:361:ILE:HA 8:E:364:GLU:CD 2.41 0.416:F:122:LYS:HA 6:F:125:LEU:CD1 2.50 0.41
1:B:3068:LEU:HB3 1:B:3078:ALA:CB 2.44 0.411:B:2690:ILE:C 1:B:3715:VAL:CB 2.89 0.41
6:F:110:LEU:HD13 6:F:124:SER:HB3 2.01 0.417:G:190:MET:SD 7:G:206:ARG:NE 2.93 0.414:H:59:LEU:O 4:H:63:ARG:N 2.54 0.415:A:1222:ASN:O 5:A:1223:VAL:C 2.58 0.415:A:1581:GLU:C 5:A:1583:LYS:N 2.74 0.415:A:2036:LEU:O 5:A:2037:TYR:C 2.59 0.415:A:635:LYS:O 5:A:636:ASP:C 2.58 0.41
1:B:2663:LEU:HD21 1:B:2678:LEU:CB 2.50 0.411:B:3553:SER:O 1:B:3555:PHE:N 2.54 0.416:F:213:LYS:HG3 6:F:214:PRO:HD3 2.02 0.416:F:71:LEU:CD1 6:F:229:LEU:HA 2.50 0.416:F:434:SER:O 6:F:435:LEU:HD12 2.20 0.416:F:487:ARG:HA 6:F:487:ARG:NE 2.36 0.41
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
6:F:6:LEU:HD23 6:F:6:LEU:HA 1.84 0.411:B:2634:TYR:H 1:B:2634:TYR:HD1 1.66 0.41
1:B:3316:TYR:CD1 1:B:3316:TYR:C 2.90 0.411:B:3418:ARG:HB2 1:B:3418:ARG:NH1 2.24 0.411:B:3663:LEU:O 1:B:3667:ILE:HG23 2.20 0.41
2:C:701:VAL:HG13 2:C:711:ASP:CB 2.51 0.418:E:390:ALA:HB1 8:E:394:TYR:CE2 2.55 0.417:G:8:LEU:HD13 7:G:10:ILE:HD11 2.03 0.417:G:18:LYS:HA 7:G:30:VAL:HA 2.02 0.416:F:61:SER:OG 7:G:270:GLU:O 2.25 0.41
7:G:351:THR:HG22 7:G:354:GLN:NE2 2.36 0.415:A:1286:GLU:O 5:A:1290:THR:N 2.34 0.411:B:3249:ILE:O 1:B:3253:LEU:HG 2.21 0.411:B:3492:LYS:O 1:B:3510:LYS:CE 2.68 0.416:F:105:GLY:O 6:F:106:ILE:HD13 2.21 0.417:G:18:LYS:HB3 7:G:30:VAL:HG22 2.02 0.415:A:566:TYR:C 5:A:568:PRO:N 2.73 0.411:B:2654:ILE:HA 1:B:2654:ILE:HD12 1.81 0.411:B:3220:PRO:C 1:B:3222:LEU:H 2.24 0.416:F:304:TRP:O 6:F:306:ARG:HG3 2.21 0.41
7:G:163:VAL:HG22 7:G:175:ILE:HG13 1.67 0.411:B:3068:LEU:HD22 1:B:3078:ALA:O 2.20 0.411:B:3464:PHE:CD2 1:B:3575:ASP:CB 3.04 0.411:B:3666:PHE:O 1:B:3669:ASP:N 2.54 0.413:D:442:UNK:O 3:D:443:UNK:C 2.69 0.418:E:361:ILE:HA 8:E:364:GLU:OE1 2.21 0.418:E:384:CYS:O 8:E:387:MET:HB2 2.20 0.41
7:G:124:PHE:CD1 7:G:359:LYS:HG2 2.56 0.417:G:149:THR:HG22 7:G:150:GLY:N 2.36 0.415:A:1044:LYS:O 5:A:1045:THR:C 2.58 0.415:A:1262:LYS:O 5:A:1265:ILE:N 2.54 0.415:A:137:LEU:O 5:A:140:PHE:N 2.51 0.416:F:397:ASP:O 6:F:401:ARG:HG3 2.21 0.41
1:B:2849:TYR:HA 1:B:2852:PHE:CB 2.50 0.411:B:3078:ALA:O 1:B:3081:ALA:HB3 2.21 0.411:B:3360:LEU:CB 1:B:3424:ARG:CG 2.99 0.411:B:3551:GLN:HA 1:B:3554:SER:HG 1.86 0.413:D:418:UNK:C 3:D:420:UNK:N 2.83 0.417:G:9:VAL:HG12 7:G:340:TRP:CD1 2.55 0.415:A:996:GLY:C 5:A:998:GLN:N 2.73 0.401:B:3038:GLU:N 1:B:3038:GLU:CD 2.73 0.40
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:3236:ARG:CD 1:B:3338:CYS:CB 2.95 0.405:A:890:TYR:O 5:A:892:ASP:N 2.54 0.40
1:B:3435:GLU:CD 1:B:3435:GLU:N 2.73 0.406:F:23:SER:HB3 6:F:163:ASP:H 1.85 0.406:F:463:GLY:O 6:F:466:HIS:HD2 2.04 0.406:F:94:LEU:HA 6:F:98:LEU:HB2 2.02 0.407:G:27:PRO:HA 7:G:340:TRP:CZ2 2.56 0.405:A:1295:GLU:O 5:A:1356:ALA:CB 2.68 0.401:B:3136:PHE:O 1:B:3141:LEU:N 2.54 0.401:B:3733:LEU:O 1:B:3733:LEU:HD23 2.21 0.405:A:2517:LEU:O 5:A:2519:LEU:N 2.54 0.401:B:2941:HIS:C 1:B:2943:ILE:N 2.74 0.401:B:3391:LEU:C 1:B:3402:SER:CB 2.87 0.401:B:3559:SER:HG 1:B:3560:TYR:H 1.67 0.406:F:466:HIS:CG 6:F:467:GLN:N 2.90 0.407:G:310:ALA:O 7:G:314:GLN:N 2.36 0.405:A:1103:LEU:C 5:A:1105:ASN:N 2.74 0.401:B:2819:GLU:C 1:B:2821:ILE:N 2.75 0.40
1:B:3071:GLU:HG2 1:B:3071:GLU:O 2.21 0.401:B:3486:GLN:C 1:B:3486:GLN:NE2 2.73 0.40
1:B:3544:PHE:CE1 1:B:3579:GLY:HA2 2.52 0.401:B:3661:THR:HA 1:B:3664:ALA:HB2 2.04 0.401:B:3668:ARG:O 1:B:3671:ILE:N 2.52 0.407:G:103:VAL:O 7:G:356:TRP:HZ3 2.05 0.404:H:183:LYS:O 4:H:185:LEU:N 2.54 0.40
There are no symmetry-related clashes.
5.3 Torsion angles i○
5.3.1 Protein backbone i○
In the following table, the Percentiles column shows the percent Ramachandran outliers of thechain as a percentile score with respect to all PDB entries followed by that with respect to all EMentries.
The Analysed column shows the number of residues for which the backbone conformation wasanalysed, and the total number of residues.
Mol Chain Analysed Favoured Allowed Outliers Percentiles
1 B 935/1115 (84%) 658 (70%) 205 (22%) 72 (8%) 1 15Continued on next page...
Page 55 Full wwPDB EM Validation Report EMD-6816, 5Y81
Continued from previous page...Mol Chain Analysed Favoured Allowed Outliers Percentiles
2 C 136/336 (40%) 99 (73%) 24 (18%) 13 (10%) 0 11
4 H 136/279 (49%) 120 (88%) 14 (10%) 2 (2%) 10 46
5 A 1857/2627 (71%) 1494 (80%) 251 (14%) 112 (6%) 1 19
6 F 417/490 (85%) 350 (84%) 62 (15%) 5 (1%) 13 50
7 G 345/375 (92%) 311 (90%) 32 (9%) 2 (1%) 25 65
8 E 39/41 (95%) 29 (74%) 10 (26%) 0 100 100
All All 3865/5263 (73%) 3061 (79%) 598 (16%) 206 (5%) 3 21
All (206) Ramachandran outliers are listed below:
Mol Chain Res Type1 B 2649 ILE1 B 2652 THR1 B 2787 PRO1 B 2788 THR1 B 3056 ALA1 B 3117 LEU1 B 3164 PRO1 B 3223 ALA1 B 3242 ASP1 B 3293 ARG1 B 3367 HIS1 B 3401 HIS1 B 3407 TYR1 B 3453 PRO1 B 3463 SER1 B 3480 PHE1 B 3481 ASP1 B 3552 TYR1 B 3592 PRO1 B 3598 PRO1 B 3657 ASN1 B 3704 ALA1 B 3742 PRO2 C 674 ALA2 C 678 HIS2 C 714 GLY2 C 715 PRO2 C 716 ARG2 C 739 SER
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Continued from previous page...Mol Chain Res Type2 C 740 PRO5 A 138 ASP5 A 218 MET5 A 231 MET5 A 240 GLN5 A 245 SER5 A 303 SER5 A 411 ILE5 A 425 GLU5 A 431 VAL5 A 517 PHE5 A 567 ALA5 A 777 PRO5 A 866 PRO5 A 924 VAL5 A 958 GLN5 A 962 PRO5 A 963 PRO5 A 968 GLU5 A 970 THR5 A 973 ASP5 A 977 ILE5 A 994 THR5 A 997 ILE5 A 1035 PHE5 A 1069 LYS5 A 1094 GLU5 A 1098 ASP5 A 1153 LEU5 A 1158 PRO5 A 1223 VAL5 A 1250 SER5 A 1293 VAL5 A 1301 PRO5 A 1346 PRO5 A 1362 SER5 A 1364 PRO5 A 1373 GLU5 A 1507 LEU5 A 1591 PRO5 A 1605 ASN5 A 1630 ARG
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Continued from previous page...Mol Chain Res Type5 A 1651 TYR5 A 1860 PHE5 A 2369 VAL5 A 2419 PRO5 A 2497 PRO5 A 2506 GLU5 A 2568 TYR5 A 2572 PRO6 F 49 ALA6 F 213 LYS6 F 445 THR7 G 16 MET1 B 2997 ASN1 B 3368 PHE1 B 3388 TYR1 B 3394 ARG1 B 3403 PHE1 B 3455 VAL1 B 3568 THR1 B 3595 ARG5 A 572 LEU5 A 959 PHE5 A 976 ALA5 A 980 PHE5 A 1011 ILE5 A 1033 ALA5 A 1037 THR5 A 1091 SER5 A 1295 GLU5 A 1653 SER5 A 2384 ILE5 A 2401 LEU5 A 2491 ILE1 B 2823 LEU1 B 3115 GLY1 B 3149 ALA1 B 3150 ASN1 B 3366 VAL1 B 3482 PRO1 B 3590 ARG1 B 3599 LEU1 B 3619 PRO
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Continued from previous page...Mol Chain Res Type1 B 3707 GLY1 B 3709 LEU1 B 3717 THR1 B 3737 ASP1 B 3743 TRP2 C 680 LEU2 C 718 HIS2 C 719 SER4 H 131 MET5 A 389 PRO5 A 426 SER5 A 889 GLN5 A 967 THR5 A 995 PRO5 A 1070 ARG5 A 1104 ASN5 A 1204 GLU5 A 1225 SER5 A 1229 PHE5 A 1302 LYS5 A 1335 SER5 A 1606 PRO5 A 1615 MET5 A 1895 LYS5 A 2226 ILE5 A 2518 GLU6 F 405 ALA1 B 2647 THR1 B 2958 ASN1 B 2962 VAL1 B 3291 TYR1 B 3356 GLY1 B 3409 ALA1 B 3410 VAL1 B 3462 VAL1 B 3706 LEU1 B 3741 MET2 C 679 ARG2 C 690 ARG4 H 129 ILE5 A 833 PRO5 A 978 ALA
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Continued from previous page...Mol Chain Res Type5 A 983 ASN5 A 986 PRO5 A 1006 SER5 A 1095 LEU5 A 1105 ASN5 A 1207 TYR5 A 1898 ASP5 A 2612 LYS6 F 70 GLU1 B 2671 GLU1 B 2942 GLU1 B 2961 ASP1 B 3054 ALA1 B 3165 GLN1 B 3219 TYR1 B 3618 GLU5 A 637 LEU5 A 1067 VAL5 A 1203 ASP5 A 1321 PRO5 A 1650 PHE5 A 1894 ILE5 A 2390 LEU5 A 2557 HIS5 A 2570 SER1 B 2789 PRO1 B 3344 PHE1 B 3602 ASN1 B 3625 THR1 B 3627 ASN2 C 675 HIS5 A 246 LEU5 A 314 ALA5 A 890 TYR5 A 991 LEU5 A 1051 LYS5 A 1583 LYS5 A 1596 LEU5 A 1647 PHE5 A 1897 GLU1 B 2902 VAL1 B 3400 VAL
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Continued from previous page...Mol Chain Res Type5 A 776 PHE5 A 993 VAL5 A 1036 PRO1 B 3393 ILE1 B 3612 PRO1 B 3381 VAL5 A 1256 ILE7 G 287 VAL5 A 982 ILE
5.3.2 Protein sidechains i○
In the following table, the Percentiles column shows the percent sidechain outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all EMentries.
The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.
Mol Chain Analysed Rotameric Outliers Percentiles
1 B 300/1012 (30%) 198 (66%) 102 (34%) 0 1
2 C 26/309 (8%) 10 (38%) 16 (62%) 0 0
5 A 7/2438 (0%) 5 (71%) 2 (29%) 0 3
6 F 372/435 (86%) 360 (97%) 12 (3%) 39 62
7 G 297/320 (93%) 284 (96%) 13 (4%) 28 54
8 E 34/34 (100%) 33 (97%) 1 (3%) 42 64
All All 1036/4548 (23%) 890 (86%) 146 (14%) 6 18
All (146) residues with a non-rotameric sidechain are listed below:
Mol Chain Res Type1 B 2636 SER1 B 2637 ILE1 B 2639 ILE1 B 2651 ASN1 B 2652 THR1 B 2654 ILE1 B 2655 ILE1 B 2663 LEU1 B 2665 LEU
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Continued from previous page...Mol Chain Res Type1 B 2674 MET1 B 2826 ILE1 B 2847 GLN1 B 2856 THR1 B 2882 GLN1 B 2885 ARG1 B 2894 ASP1 B 2896 ASN1 B 2897 MET1 B 2898 TRP1 B 2899 ASN1 B 2900 ASP1 B 2902 VAL1 B 2906 GLN1 B 2912 ILE1 B 2941 HIS1 B 2946 VAL1 B 2952 HIS1 B 2965 SER1 B 2966 GLN1 B 2967 LEU1 B 2970 ILE1 B 2971 TYR1 B 3007 SER1 B 3019 LYS1 B 3023 PHE1 B 3038 GLU1 B 3041 GLN1 B 3059 GLN1 B 3062 PHE1 B 3066 ARG1 B 3067 ARG1 B 3069 SER1 B 3095 SER1 B 3097 ILE1 B 3099 GLU1 B 3100 LEU1 B 3104 ILE1 B 3105 LEU1 B 3107 LEU1 B 3108 ILE1 B 3111 ASP
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Continued from previous page...Mol Chain Res Type1 B 3143 SER1 B 3145 SER1 B 3162 SER1 B 3167 LEU1 B 3168 HIS1 B 3169 PHE1 B 3171 LEU1 B 3172 ARG1 B 3219 TYR1 B 3229 LEU1 B 3236 ARG1 B 3247 ARG1 B 3317 TRP1 B 3318 ARG1 B 3367 HIS1 B 3411 ARG1 B 3417 GLU1 B 3418 ARG1 B 3421 GLN1 B 3422 LEU1 B 3424 ARG1 B 3427 ASN1 B 3432 LYS1 B 3435 GLU1 B 3440 SER1 B 3443 PHE1 B 3444 ASN1 B 3449 ILE1 B 3462 VAL1 B 3467 LEU1 B 3468 HIS1 B 3472 ASN1 B 3474 PHE1 B 3484 ASP1 B 3485 ILE1 B 3486 GLN1 B 3487 ASP1 B 3488 PHE1 B 3489 MET1 B 3492 LYS1 B 3494 ASN1 B 3499 ASP
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Continued from previous page...Mol Chain Res Type1 B 3552 TYR1 B 3568 THR1 B 3570 HIS1 B 3571 LYS1 B 3611 SER1 B 3647 THR1 B 3652 LEU1 B 3668 ARG1 B 3674 TRP2 C 680 LEU2 C 681 THR2 C 684 TYR2 C 685 LEU2 C 687 ASN2 C 688 ILE2 C 689 GLU2 C 694 TRP2 C 695 GLN2 C 696 CYS2 C 697 PHE2 C 699 ARG2 C 702 GLN2 C 703 LEU2 C 706 ARG2 C 707 PHE5 A 948 ILE5 A 1896 LEU6 F 47 TYR6 F 56 ILE6 F 66 ARG6 F 67 LYS6 F 70 GLU6 F 72 LYS6 F 125 LEU6 F 128 LEU6 F 137 CYS6 F 213 LYS6 F 440 LEU6 F 442 THR7 G 16 MET7 G 71 ILE7 G 73 HIS
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Continued from previous page...Mol Chain Res Type7 G 135 SER7 G 136 ILE7 G 137 GLN7 G 139 VAL7 G 151 ILE7 G 152 VAL7 G 153 LEU7 G 159 VAL7 G 163 VAL7 G 288 ASP8 E 394 TYR
Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (26)such sidechains are listed below:
Mol Chain Res Type1 B 2752 HIS1 B 2941 HIS1 B 3041 GLN1 B 3367 HIS1 B 3427 ASN1 B 3444 ASN1 B 3486 GLN1 B 3494 ASN1 B 3497 HIS1 B 3515 ASN1 B 3570 HIS1 B 3732 ASN2 C 687 ASN6 F 89 GLN6 F 91 GLN6 F 96 ASN6 F 120 ASN6 F 162 HIS6 F 234 ASN6 F 248 HIS6 F 406 HIS6 F 444 HIS6 F 449 GLN7 G 115 ASN7 G 280 ASN8 E 377 HIS
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5.3.3 RNA i○
There are no RNA molecules in this entry.
5.4 Non-standard residues in protein, DNA, RNA chains i○
There are no non-standard protein/DNA/RNA residues in this entry.
5.5 Carbohydrates i○
There are no monosaccharides in this entry.
5.6 Ligand geometry i○
There are no ligands in this entry.
5.7 Other polymers i○
There are no such residues in this entry.
5.8 Polymer linkage issues i○
There are no chain breaks in this entry.
Page 66 Full wwPDB EM Validation Report EMD-6816, 5Y81
6 Map visualisation i○
This section contains visualisations of the EMDB entry EMD-6816. These allow visual inspectionof the internal detail of the map and identification of artifacts.
No raw map or half-maps were deposited for this entry and therefore no images, graphs, etc.pertaining to the raw map can be shown.
6.1 Orthogonal projections i○
6.1.1 Primary map
X Y Z
The images above show the map projected in three orthogonal directions.
6.2 Central slices i○
6.2.1 Primary map
X Index: 144 Y Index: 144 Z Index: 144
Page 67 Full wwPDB EM Validation Report EMD-6816, 5Y81
The images above show central slices of the map in three orthogonal directions.
6.3 Largest variance slices i○
6.3.1 Primary map
X Index: 158 Y Index: 153 Z Index: 160
The images above show the largest variance slices of the map in three orthogonal directions.
6.4 Orthogonal surface views i○
6.4.1 Primary map
X Y Z
The images above show the 3D surface view of the map at the recommended contour level 0.0225.These images, in conjunction with the slice images, may facilitate assessment of whether an ap-propriate contour level has been provided.
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6.5 Mask visualisation i○
This section was not generated. No masks/segmentation were deposited.
Page 69 Full wwPDB EM Validation Report EMD-6816, 5Y81
7 Map analysis i○
This section contains the results of statistical analysis of the map.
7.1 Map-value distribution i○
The map-value distribution is plotted in 128 intervals along the x-axis. The y-axis is logarithmic.A spike in this graph at zero usually indicates that the volume has been masked.
Page 70 Full wwPDB EM Validation Report EMD-6816, 5Y81
7.2 Volume estimate i○
The volume at the recommended contour level is 378 nm3; this corresponds to an approximatemass of 341 kDa.
The volume estimate graph shows how the enclosed volume varies with the contour level. Therecommended contour level is shown as a vertical line and the intersection between the line andthe curve gives the volume of the enclosed surface at the given level.
Page 71 Full wwPDB EM Validation Report EMD-6816, 5Y81
7.3 Rotationally averaged power spectrum i○
*Reported resolution corresponds to spatial frequency of 0.213 Å−1
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8 Fourier-Shell correlation i○
This section was not generated. No FSC curve or half-maps provided.
Page 73 Full wwPDB EM Validation Report EMD-6816, 5Y81
9 Map-model fit i○
This section contains information regarding the fit between EMDB map EMD-6816 and PDBmodel 5Y81. Per-residue inclusion information can be found in section 3 on page 5.
9.1 Map-model overlay i○
X Y Z
The images above show the 3D surface view of the map at the recommended contour level 0.0225at 50% transparency in yellow overlaid with a ribbon representation of the model coloured in blue.These images allow for the visual assessment of the quality of fit between the atomic model andthe map.
Page 74 Full wwPDB EM Validation Report EMD-6816, 5Y81
9.2 Atom inclusion i○
At the recommended contour level, 96% of all backbone atoms, 85% of all non-hydrogen atoms,are inside the map.