Full wwPDB/EMDataBank EM Map/Model Validation Report · 2018. 2. 24. · m1 r2 e3 c4 i5 q15 n18 p32 m36 p37 ser asp lys thr ile gly gly gly asp d47 t51 s54 p63 r64 f67 l86 f87 h88

Full wwPDB EM Validation Report i○

Dec 6, 2020 – 08:02 AM EST

PDB ID : 5JCOEMDB ID : EMD-8150

Title : Structure and dynamics of single-isoform recombinant neuronal human tubulinAuthors : Vemu, A.; Atherton, J.; Spector, J.O.; Szyk, A.; Moores, C.A.; Roll-Mecak,

A.Deposited on : 2016-04-15

Resolution : 4.00 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.dev61Mogul : 1.8.5 (274361), CSD as541be (2020)

MolProbity : 4.02b-467buster-report : 1.1.7 (2018)

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

https://www.wwpdb.org/validation/2017/EMValidationReportHelp



https://www.wwpdb.org/validation/2017/EMValidationReportHelp#references

Page 2 Full wwPDB EM Validation Report EMD-8150, 5JCO

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 4.00 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 C 426

1 D 426

1 I 426

1 J 426

1 K 426

1 L 426

2 A 437

2 B 437Continued on next page...

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#overall_quality


Continued from previous page...Mol Chain Length Quality of chain

2 E 437

2 F 437

2 G 437

2 H 437


2 Entry composition i○

There are 5 unique types of molecules in this entry. The entry contains 40512 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 Tubulin beta-3 chain.

Mol Chain Residues Atoms AltConf Trace

1 K 426 Total C N O S3341 2103 571 642 25 0 0

1 I 426 Total C N O S3341 2103 571 642 25 0 0

1 J 426 Total C N O S3341 2103 571 642 25 0 0

1 C 426 Total C N O S3341 2103 571 642 25 0 0

1 D 426 Total C N O S3341 2103 571 642 25 0 0

1 L 426 Total C N O S3341 2103 571 642 25 0 0

• Molecule 2 is a protein called Tubulin alpha-1A chain.

Mol Chain Residues Atoms AltConf Trace

2 H 428 Total C N O S3345 2124 571 629 21 0 0

2 E 428 Total C N O S3345 2124 571 629 21 0 0

2 F 428 Total C N O S3345 2124 571 629 21 0 0

2 A 428 Total C N O S3345 2124 571 629 21 0 0

2 B 428 Total C N O S3345 2124 571 629 21 0 0

2 G 428 Total C N O S3345 2124 571 629 21 0 0

• Molecule 3 is PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER (three-letter code: G2P) (formula: C11H18N5O13P3).

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#entry_composition


Mol Chain Residues Atoms AltConf

3 K 1 Total C N O P32 11 5 13 3 0

3 I 1 Total C N O P32 11 5 13 3 0

3 J 1 Total C N O P32 11 5 13 3 0

3 C 1 Total C N O P32 11 5 13 3 0

3 D 1 Total C N O P32 11 5 13 3 0

3 L 1 Total C N O P32 11 5 13 3 0

• Molecule 4 is MAGNESIUM ION (three-letter code: MG) (formula: Mg).


4 G 1 Total Mg1 1 0

4 J 1 Total Mg1 1 0

4 D 1 Total Mg1 1 0

4 K 1 Total Mg1 1 0

4 E 1 Total Mg1 1 0

4 H 1 Total Mg1 1 0

Continued on next page...


Continued from previous page...Mol Chain Residues Atoms AltConf

4 B 1 Total Mg1 1 0

4 I 1 Total Mg1 1 0

4 C 1 Total Mg1 1 0

4 A 1 Total Mg1 1 0

4 L 1 Total Mg1 1 0

4 F 1 Total Mg1 1 0

• Molecule 5 is GUANOSINE-5’-TRIPHOSPHATE (three-letter code: GTP) (formula:C10H16N5O14P3).


5 H 1 Total C N O P32 10 5 14 3 0

5 E 1 Total C N O P32 10 5 14 3 0

5 F 1 Total C N O P32 10 5 14 3 0

5 A 1 Total C N O P32 10 5 14 3 0

5 B 1 Total C N O P32 10 5 14 3 0



Continued from previous page...Mol Chain Residues Atoms AltConf

5 G 1 Total C N O P32 10 5 14 3 0


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: Tubulin beta-3 chain

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https://www.wwpdb.org/validation/2017/EMValidationReportHelp#residue_plots


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• Molecule 2: Tubulin alpha-1A chain

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4 Experimental information i○

Property Value SourceEM reconstruction method HELICAL DepositorImposed symmetry HELICAL, twist=-25.71◦, rise=8.86 Å, axial

sym=C14Depositor

Number of segments used 10164 DepositorResolution determination method OTHER DepositorCTF correction method PHASE FLIPPING AND AMPLITUDE

CORRECTIONDepositor

Microscope FEI POLARA 300 DepositorVoltage (kV) 300 DepositorElectron dose (e−/Å2

) 25 DepositorMinimum defocus (nm) Not providedMaximum defocus (nm) Not providedMagnification Not providedImage detector DIRECT ELECTRON DE-20 (5k x 3k) DepositorMaximum map value 0.172 DepositorMinimum map value -0.091 DepositorAverage map value 0.004 DepositorMap value standard deviation 0.016 DepositorRecommended contour level 0.043 DepositorMap size (Å) 202.52, 97.600006, 253.76001 wwPDBMap dimensions 166, 80, 208 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.22, 1.22, 1.22 Depositor

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#experimental_info


5 Model quality i○

5.1 Standard geometry i○

Bond lengths and bond angles in the following residue types are not validated in this section: GTP,MG, G2P

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 C 0.48 0/3416 0.75 0/46281 D 0.48 0/3416 0.75 0/46281 I 0.49 0/3416 0.75 0/46281 J 0.48 0/3416 0.75 0/46281 K 0.49 0/3416 0.75 0/46281 L 0.49 0/3416 0.75 0/46282 A 0.49 0/3422 0.91 1/4647 (0.0%)2 B 0.49 0/3422 0.85 1/4647 (0.0%)2 E 0.49 0/3422 0.90 1/4647 (0.0%)2 F 0.48 0/3422 0.85 1/4647 (0.0%)2 G 0.48 0/3422 0.86 1/4647 (0.0%)2 H 0.49 0/3422 0.86 1/4647 (0.0%)All All 0.49 0/41028 0.81 6/55650 (0.0%)

There are no bond length outliers.

All (6) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 A 36 MET C-N-CD -32.97 48.07 120.602 E 36 MET C-N-CD -30.94 52.53 120.602 H 36 MET C-N-CD -26.49 62.33 120.602 G 36 MET C-N-CD -25.84 63.75 120.602 B 36 MET C-N-CD -25.00 65.61 120.602 F 36 MET C-N-CD -24.94 65.73 120.60

There are no chirality outliers.

There are no planarity outliers.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#model_quality

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#standard_geometry


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 C 3341 0 3224 38 01 D 3341 0 3224 38 01 I 3341 0 3224 49 01 J 3341 0 3224 39 01 K 3341 0 3224 49 01 L 3341 0 3224 49 02 A 3345 0 3259 62 02 B 3345 0 3259 64 02 E 3345 0 3259 71 02 F 3345 0 3259 62 02 G 3345 0 3259 72 02 H 3345 0 3259 72 03 C 32 0 14 0 03 D 32 0 14 0 03 I 32 0 14 0 03 J 32 0 14 0 03 K 32 0 14 0 03 L 32 0 14 0 04 A 1 0 0 0 04 B 1 0 0 0 04 C 1 0 0 0 04 D 1 0 0 0 04 E 1 0 0 0 04 F 1 0 0 0 04 G 1 0 0 0 04 H 1 0 0 0 04 I 1 0 0 0 04 J 1 0 0 0 04 K 1 0 0 0 04 L 1 0 0 0 05 A 32 0 12 1 05 B 32 0 12 1 05 E 32 0 12 1 05 F 32 0 12 1 05 G 32 0 12 1 05 H 32 0 12 1 0All All 40512 0 39054 582 0

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#close_contacts


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 7.

All (582) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

2:G:324:VAL:HG23 2:G:327:ASP:HB2 1.60 0.842:H:324:VAL:HG23 2:H:327:ASP:HB2 1.60 0.842:F:324:VAL:HG23 2:F:327:ASP:HB2 1.60 0.842:B:324:VAL:HG23 2:B:327:ASP:HB2 1.60 0.832:E:324:VAL:HG23 2:E:327:ASP:HB2 1.60 0.832:A:324:VAL:HG23 2:A:327:ASP:HB2 1.60 0.831:C:317:PHE:HB3 1:C:321:MET:HE1 1.60 0.821:I:317:PHE:HB3 1:I:321:MET:HE1 1.60 0.821:J:317:PHE:HB3 1:J:321:MET:HE1 1.61 0.801:L:317:PHE:HB3 1:L:321:MET:HE1 1.61 0.801:D:317:PHE:HB3 1:D:321:MET:HE1 1.61 0.801:K:317:PHE:HB3 1:K:321:MET:HE1 1.61 0.801:L:177:ASP:O 2:G:352:LYS:HD2 1.84 0.781:I:177:ASP:O 2:E:352:LYS:HD2 1.84 0.781:K:177:ASP:O 2:H:352:LYS:HD2 1.84 0.75

1:K:175:VAL:HG11 2:H:329:ASN:ND2 2.01 0.751:L:175:VAL:HG11 2:G:329:ASN:ND2 2.02 0.741:I:175:VAL:HG11 2:E:329:ASN:ND2 2.02 0.741:C:317:PHE:HB3 1:C:321:MET:CE 2.20 0.721:I:317:PHE:HB3 1:I:321:MET:CE 2.20 0.721:D:317:PHE:HB3 1:D:321:MET:CE 2.20 0.711:K:317:PHE:HB3 1:K:321:MET:CE 2.20 0.712:G:242:LEU:HD11 2:G:252:LEU:HD13 1.73 0.712:A:242:LEU:HD11 2:A:252:LEU:HD13 1.73 0.712:E:242:LEU:HD11 2:E:252:LEU:HD13 1.73 0.712:F:242:LEU:HD11 2:F:252:LEU:HD13 1.73 0.712:H:242:LEU:HD11 2:H:252:LEU:HD13 1.73 0.711:J:317:PHE:HB3 1:J:321:MET:CE 2.20 0.712:B:242:LEU:HD11 2:B:252:LEU:HD13 1.73 0.711:L:317:PHE:HB3 1:L:321:MET:CE 2.20 0.712:E:259:LEU:HD11 2:E:316:CYS:SG 2.31 0.692:H:259:LEU:HD11 2:H:316:CYS:SG 2.31 0.692:B:259:LEU:HD11 2:B:316:CYS:SG 2.31 0.692:A:259:LEU:HD11 2:A:316:CYS:SG 2.31 0.692:G:259:LEU:HD11 2:G:316:CYS:SG 2.31 0.692:F:259:LEU:HD11 2:F:316:CYS:SG 2.31 0.691:L:178:THR:OG1 1:L:181:GLU:HG3 1.93 0.69



Continued from previous page...


Clashoverlap (Å)

1:J:178:THR:OG1 1:J:181:GLU:HG3 1.93 0.681:I:178:THR:OG1 1:I:181:GLU:HG3 1.93 0.681:C:178:THR:OG1 1:C:181:GLU:HG3 1.93 0.681:K:178:THR:OG1 1:K:181:GLU:HG3 1.93 0.671:D:178:THR:OG1 1:D:181:GLU:HG3 1.93 0.672:G:210:TYR:O 2:G:213:CYS:SG 2.48 0.651:I:141:GLY:O 1:I:145:SER:OG 2.07 0.651:K:141:GLY:O 1:K:145:SER:OG 2.07 0.651:C:141:GLY:O 1:C:145:SER:OG 2.07 0.651:D:141:GLY:O 1:D:145:SER:OG 2.07 0.651:I:175:VAL:CG1 2:E:329:ASN:OD1 2.45 0.651:K:175:VAL:CG1 2:H:329:ASN:OD1 2.45 0.641:I:175:VAL:HG11 2:E:329:ASN:HD21 1.63 0.641:K:175:VAL:HG11 2:H:329:ASN:HD21 1.62 0.641:I:175:VAL:HG11 2:E:329:ASN:CG 2.17 0.641:L:175:VAL:HG11 2:G:329:ASN:OD1 1.97 0.641:L:175:VAL:CG1 2:G:329:ASN:OD1 2.45 0.641:K:175:VAL:HG11 2:H:329:ASN:OD1 1.98 0.641:I:175:VAL:HG11 2:E:329:ASN:OD1 1.97 0.642:F:394:LYS:HG3 1:L:346:PRO:HG3 1.79 0.641:K:175:VAL:HG11 2:H:329:ASN:CG 2.17 0.631:K:346:PRO:HG3 2:B:394:LYS:HG3 1.78 0.632:E:394:LYS:HG3 1:C:346:PRO:HG3 1.80 0.631:L:175:VAL:HG11 2:G:329:ASN:CG 2.17 0.632:F:407:TRP:O 2:F:411:GLU:HG2 1.99 0.632:G:407:TRP:O 2:G:411:GLU:HG2 1.99 0.631:I:346:PRO:HG3 2:A:394:LYS:HG3 1.81 0.622:A:407:TRP:O 2:A:411:GLU:HG2 1.99 0.622:E:407:TRP:O 2:E:411:GLU:HG2 1.99 0.622:B:407:TRP:O 2:B:411:GLU:HG2 1.99 0.622:H:407:TRP:O 2:H:411:GLU:HG2 1.99 0.62

1:L:175:VAL:HG11 2:G:329:ASN:HD21 1.63 0.612:H:394:LYS:HG3 1:D:346:PRO:HG3 1.81 0.60

2:E:3:GLU:O 2:E:132:LEU:HB2 2.01 0.591:J:346:PRO:HG3 2:G:394:LYS:HG3 1.83 0.59

2:A:3:GLU:O 2:A:132:LEU:HB2 2.02 0.592:H:3:GLU:O 2:H:132:LEU:HB2 2.01 0.592:B:3:GLU:O 2:B:132:LEU:HB2 2.02 0.592:G:3:GLU:O 2:G:132:LEU:HB2 2.01 0.592:F:3:GLU:O 2:F:132:LEU:HB2 2.02 0.59

2:E:324:VAL:HG23 2:E:327:ASP:CB 2.32 0.58Continued on next page...




Clashoverlap (Å)

2:H:324:VAL:HG23 2:H:327:ASP:CB 2.32 0.582:A:324:VAL:HG23 2:A:327:ASP:CB 2.33 0.582:F:129:CYS:SG 2:F:130:THR:N 2.76 0.582:G:129:CYS:SG 2:G:130:THR:N 2.76 0.58

2:G:324:VAL:HG23 2:G:327:ASP:CB 2.32 0.582:A:129:CYS:SG 2:A:130:THR:N 2.77 0.582:E:5:ILE:HG22 2:E:64:ARG:HB3 1.84 0.582:A:5:ILE:HG22 2:A:64:ARG:HB3 1.84 0.572:B:5:ILE:HG22 2:B:64:ARG:HB3 1.84 0.572:E:129:CYS:SG 2:E:130:THR:N 2.77 0.572:F:5:ILE:HG22 2:F:64:ARG:HB3 1.84 0.57

2:B:324:VAL:HG23 2:B:327:ASP:CB 2.33 0.572:G:5:ILE:HG22 2:G:64:ARG:HB3 1.84 0.572:H:5:ILE:HG22 2:H:64:ARG:HB3 1.84 0.57

2:F:324:VAL:HG23 2:F:327:ASP:CB 2.33 0.572:E:88:HIS:O 2:E:91:GLN:HG2 2.05 0.57

2:G:324:VAL:CG2 2:G:327:ASP:HB2 2.33 0.572:H:88:HIS:O 2:H:91:GLN:HG2 2.05 0.57

2:H:324:VAL:CG2 2:H:327:ASP:HB2 2.33 0.572:A:88:HIS:O 2:A:91:GLN:HG2 2.05 0.572:B:88:HIS:O 2:B:91:GLN:HG2 2.05 0.57

2:F:324:VAL:CG2 2:F:327:ASP:HB2 2.33 0.572:B:129:CYS:SG 2:B:130:THR:N 2.77 0.572:E:324:VAL:CG2 2:E:327:ASP:HB2 2.33 0.562:H:129:CYS:SG 2:H:130:THR:N 2.77 0.562:B:324:VAL:CG2 2:B:327:ASP:HB2 2.33 0.56

2:F:88:HIS:O 2:F:91:GLN:HG2 2.05 0.562:G:88:HIS:O 2:G:91:GLN:HG2 2.05 0.56

2:A:324:VAL:CG2 2:A:327:ASP:HB2 2.33 0.562:E:210:TYR:O 2:E:213:CYS:SG 2.48 0.562:A:210:TYR:O 2:A:213:CYS:SG 2.48 0.562:H:283:HIS:CB 2:E:88:HIS:HB3 2.36 0.562:F:394:LYS:HG3 1:L:346:PRO:CG 2.36 0.552:B:210:TYR:O 2:B:213:CYS:SG 2.48 0.552:G:63:PRO:HD3 2:G:86:LEU:HD12 1.89 0.552:H:210:TYR:O 2:H:213:CYS:SG 2.48 0.552:A:88:HIS:HB3 2:B:283:HIS:CB 2.37 0.552:F:63:PRO:HD3 2:F:86:LEU:HD12 1.89 0.552:B:63:PRO:HD3 2:B:86:LEU:HD12 1.89 0.552:G:173:PRO:HB3 2:G:183:GLU:OE1 2.07 0.552:B:147:SER:OG 2:B:190:THR:HB 2.07 0.54





Clashoverlap (Å)

2:F:173:PRO:HB3 2:F:183:GLU:OE1 2.07 0.542:H:147:SER:OG 2:H:190:THR:HB 2.07 0.542:A:147:SER:OG 2:A:190:THR:HB 2.07 0.541:I:255:VAL:HG11 2:A:100:ALA:O 2.08 0.542:A:2:ARG:HB3 2:A:133:GLN:NE2 2.23 0.542:E:147:SER:OG 2:E:190:THR:HB 2.07 0.542:F:210:TYR:O 2:F:213:CYS:SG 2.48 0.542:H:2:ARG:HB3 2:H:133:GLN:NE2 2.23 0.542:F:100:ALA:O 1:L:255:VAL:HG11 2.07 0.541:I:346:PRO:CG 2:A:394:LYS:HG3 2.37 0.542:E:394:LYS:HG3 1:C:346:PRO:CG 2.37 0.542:E:2:ARG:HB3 2:E:133:GLN:NE2 2.23 0.542:G:2:ARG:HB3 2:G:133:GLN:NE2 2.23 0.541:K:346:PRO:CG 2:B:394:LYS:HG3 2.37 0.542:A:63:PRO:HD3 2:A:86:LEU:HD12 1.90 0.542:B:2:ARG:HB3 2:B:133:GLN:NE2 2.23 0.542:F:2:ARG:HB3 2:F:133:GLN:NE2 2.23 0.542:H:63:PRO:HD3 2:H:86:LEU:HD12 1.89 0.542:F:147:SER:OG 2:F:190:THR:HB 2.07 0.542:G:147:SER:OG 2:G:190:THR:HB 2.07 0.541:I:203:ASP:OD2 1:I:302:ALA:HB2 2.08 0.542:A:173:PRO:HB3 2:A:183:GLU:OE1 2.07 0.542:E:173:PRO:HB3 2:E:183:GLU:OE1 2.07 0.542:F:283:HIS:CB 2:B:88:HIS:HB3 2.38 0.542:E:100:ALA:O 1:C:255:VAL:HG11 2.08 0.54

1:D:203:ASP:OD2 1:D:302:ALA:HB2 2.08 0.541:K:203:ASP:OD2 1:K:302:ALA:HB2 2.08 0.541:C:203:ASP:OD2 1:C:302:ALA:HB2 2.08 0.542:E:63:PRO:HD3 2:E:86:LEU:HD12 1.90 0.541:L:176:SER:OG 2:G:349:THR:HB 2.08 0.541:D:110:ALA:O 1:D:113:VAL:HG12 2.08 0.532:H:88:HIS:HB3 2:G:283:HIS:CB 2.38 0.531:J:203:ASP:OD2 1:J:302:ALA:HB2 2.08 0.531:K:110:ALA:O 1:K:113:VAL:HG12 2.08 0.531:L:203:ASP:OD2 1:L:302:ALA:HB2 2.08 0.531:I:110:ALA:O 1:I:113:VAL:HG12 2.08 0.531:C:110:ALA:O 1:C:113:VAL:HG12 2.08 0.531:I:286:VAL:HB 1:I:287:PRO:HD3 1.89 0.53

2:H:173:PRO:HB3 2:H:183:GLU:OE1 2.07 0.532:B:173:PRO:HB3 2:B:183:GLU:OE1 2.07 0.531:D:12:CYS:SG 1:D:13:GLY:N 2.81 0.53





Clashoverlap (Å)

2:F:332:ILE:HG23 2:F:351:PHE:CD2 2.44 0.532:H:209:ILE:HG21 2:H:227:LEU:HG 1.91 0.531:K:12:CYS:SG 1:K:13:GLY:N 2.81 0.531:C:286:VAL:HB 1:C:287:PRO:HD3 1.90 0.532:G:332:ILE:HG23 2:G:351:PHE:CD2 2.44 0.531:K:286:VAL:HB 1:K:287:PRO:HD3 1.89 0.532:A:332:ILE:HG23 2:A:351:PHE:CD2 2.44 0.531:D:286:VAL:HB 1:D:287:PRO:HD3 1.89 0.531:I:176:SER:OG 2:E:349:THR:HB 2.08 0.531:J:110:ALA:O 1:J:113:VAL:HG12 2.08 0.53

2:E:332:ILE:HG23 2:E:351:PHE:CD2 2.44 0.522:E:32:PRO:O 2:E:86:LEU:HD23 2.09 0.52

1:K:176:SER:OG 2:H:349:THR:HB 2.08 0.521:K:344:TRP:CD1 1:K:345:ILE:HG13 2.44 0.521:L:286:VAL:HB 1:L:287:PRO:HD3 1.89 0.521:C:12:CYS:SG 1:C:13:GLY:N 2.81 0.521:J:12:CYS:SG 1:J:13:GLY:N 2.81 0.521:J:286:VAL:HB 1:J:287:PRO:HD3 1.89 0.521:L:110:ALA:O 1:L:113:VAL:HG12 2.08 0.521:L:12:CYS:SG 1:L:13:GLY:N 2.81 0.52

2:B:209:ILE:HG21 2:B:227:LEU:HG 1.92 0.521:C:344:TRP:CD1 1:C:345:ILE:HG13 2.45 0.521:D:344:TRP:CD1 1:D:345:ILE:HG13 2.45 0.522:H:32:PRO:O 2:H:86:LEU:HD23 2.09 0.52

2:H:332:ILE:HG23 2:H:351:PHE:CD2 2.44 0.521:I:69:GLU:HG3 1:I:96:GLY:HA3 1.91 0.521:L:344:TRP:CD1 1:L:345:ILE:HG13 2.45 0.522:A:32:PRO:O 2:A:86:LEU:HD23 2.09 0.52

2:B:332:ILE:HG23 2:B:351:PHE:CD2 2.44 0.522:F:32:PRO:O 2:F:86:LEU:HD23 2.09 0.522:G:32:PRO:O 2:G:86:LEU:HD23 2.09 0.521:I:12:CYS:SG 1:I:13:GLY:N 2.81 0.52

1:I:344:TRP:CD1 1:I:345:ILE:HG13 2.45 0.521:J:344:TRP:CD1 1:J:345:ILE:HG13 2.45 0.522:B:32:PRO:O 2:B:86:LEU:HD23 2.09 0.52

1:K:255:VAL:HG11 2:B:100:ALA:O 2.10 0.521:K:69:GLU:HG3 1:K:96:GLY:HA3 1.91 0.521:L:69:GLU:HG3 1:L:96:GLY:HA3 1.91 0.521:C:69:GLU:HG3 1:C:96:GLY:HA3 1.91 0.521:D:69:GLU:HG3 1:D:96:GLY:HA3 1.91 0.522:F:199:ASP:OD1 2:F:256:GLN:NE2 2.43 0.52





Clashoverlap (Å)

2:A:199:ASP:OD1 2:A:256:GLN:NE2 2.43 0.522:B:199:ASP:OD1 2:B:256:GLN:NE2 2.43 0.521:J:69:GLU:HG3 1:J:96:GLY:HA3 1.91 0.521:K:346:PRO:HG3 2:B:394:LYS:CG 2.40 0.522:F:209:ILE:HG21 2:F:227:LEU:HG 1.92 0.512:E:199:ASP:OD1 2:E:256:GLN:NE2 2.43 0.512:G:199:ASP:OD1 2:G:256:GLN:NE2 2.43 0.512:G:209:ILE:HG21 2:G:227:LEU:HG 1.92 0.512:E:209:ILE:HG21 2:E:227:LEU:HG 1.91 0.512:E:394:LYS:CG 1:C:346:PRO:HG3 2.40 0.512:H:199:ASP:OD1 2:H:256:GLN:NE2 2.43 0.512:A:209:ILE:HG21 2:A:227:LEU:HG 1.92 0.512:G:129:CYS:SG 2:G:132:LEU:HB3 2.51 0.512:H:394:LYS:HG3 1:D:346:PRO:CG 2.40 0.512:F:394:LYS:CG 1:L:346:PRO:HG3 2.39 0.512:E:5:ILE:HD11 2:E:135:PHE:CE1 2.46 0.512:F:129:CYS:SG 2:F:132:LEU:HB3 2.51 0.512:G:5:ILE:HD11 2:G:135:PHE:CE1 2.46 0.512:H:129:CYS:SG 2:H:132:LEU:HB3 2.51 0.511:J:346:PRO:CG 2:G:394:LYS:HG3 2.40 0.512:B:129:CYS:SG 2:B:132:LEU:HB3 2.51 0.511:I:177:ASP:O 2:E:352:LYS:CD 2.58 0.511:I:46:ARG:O 1:I:49:VAL:HG12 2.11 0.511:C:46:ARG:O 1:C:49:VAL:HG12 2.11 0.511:D:46:ARG:O 1:D:49:VAL:HG12 2.11 0.512:F:5:ILE:HD11 2:F:135:PHE:CE1 2.46 0.512:H:5:ILE:HD11 2:H:135:PHE:CE1 2.46 0.511:K:46:ARG:O 1:K:49:VAL:HG12 2.11 0.512:A:129:CYS:SG 2:A:132:LEU:HB3 2.51 0.501:I:346:PRO:HG3 2:A:394:LYS:CG 2.41 0.502:A:5:ILE:HD11 2:A:135:PHE:CE1 2.46 0.502:E:129:CYS:SG 2:E:132:LEU:HB3 2.51 0.502:E:175:PRO:HG2 2:E:390:ARG:HD3 1.93 0.502:A:175:PRO:HG2 2:A:390:ARG:HD3 1.93 0.502:B:5:ILE:HD11 2:B:135:PHE:CE1 2.47 0.501:L:46:ARG:O 1:L:49:VAL:HG12 2.11 0.50

2:B:93:ILE:HD12 2:B:93:ILE:N 2.27 0.502:F:93:ILE:N 2:F:93:ILE:HD12 2.27 0.50

2:G:93:ILE:HD12 2:G:93:ILE:N 2.27 0.501:J:141:GLY:O 1:J:145:SER:OG 2.07 0.501:J:46:ARG:O 1:J:49:VAL:HG12 2.11 0.50





Clashoverlap (Å)

1:L:141:GLY:O 1:L:145:SER:OG 2.07 0.502:B:175:PRO:HG2 2:B:390:ARG:HD3 1.93 0.502:H:175:PRO:HG2 2:H:390:ARG:HD3 1.93 0.50

2:H:93:ILE:N 2:H:93:ILE:HD12 2.27 0.502:H:100:ALA:O 1:D:255:VAL:HG11 2.12 0.502:E:93:ILE:HD12 2:E:93:ILE:N 2.26 0.501:J:255:VAL:HG11 2:G:100:ALA:O 2.12 0.502:F:175:PRO:HG2 2:F:390:ARG:HD3 1.93 0.492:G:271:THR:HG22 2:G:377:MET:HB3 1.93 0.492:A:93:ILE:HD12 2:A:93:ILE:N 2.26 0.491:D:138:SER:HA 1:D:169:VAL:HG22 1.95 0.492:G:175:PRO:HG2 2:G:390:ARG:HD3 1.93 0.491:J:138:SER:HA 1:J:169:VAL:HG22 1.95 0.491:K:177:ASP:O 2:H:352:LYS:CD 2.58 0.491:C:138:SER:HA 1:C:169:VAL:HG22 1.95 0.49

2:E:271:THR:HG22 2:E:377:MET:HB3 1.93 0.492:A:183:GLU:N 2:A:184:PRO:CD 2.75 0.491:D:3:GLU:HB3 1:D:62:ARG:NH1 2.27 0.492:F:183:GLU:N 2:F:184:PRO:CD 2.75 0.49

2:F:271:THR:HG22 2:F:377:MET:HB3 1.93 0.492:G:183:GLU:N 2:G:184:PRO:CD 2.75 0.491:K:3:GLU:HB3 1:K:62:ARG:NH1 2.27 0.491:L:138:SER:HA 1:L:169:VAL:HG22 1.95 0.49

2:A:271:THR:HG22 2:A:377:MET:HB3 1.93 0.492:E:183:GLU:N 2:E:184:PRO:CD 2.76 0.491:K:138:SER:HA 1:K:169:VAL:HG22 1.95 0.491:C:317:PHE:CB 1:C:321:MET:CE 2.91 0.491:D:317:PHE:CB 1:D:321:MET:CE 2.91 0.491:I:138:SER:HA 1:I:169:VAL:HG22 1.95 0.491:I:317:PHE:CB 1:I:321:MET:CE 2.91 0.491:K:317:PHE:CB 1:K:321:MET:CE 2.91 0.491:L:177:ASP:O 2:G:352:LYS:CD 2.58 0.49

2:A:315:CYS:HB2 2:A:351:PHE:HD1 1.78 0.492:E:315:CYS:HB2 2:E:351:PHE:HD1 1.78 0.492:H:271:THR:HG22 2:H:377:MET:HB3 1.93 0.492:H:394:LYS:CG 1:D:346:PRO:HG3 2.43 0.491:L:3:GLU:HB3 1:L:62:ARG:NH1 2.27 0.492:H:183:GLU:N 2:H:184:PRO:CD 2.75 0.492:B:183:GLU:N 2:B:184:PRO:CD 2.75 0.49

2:B:271:THR:HG22 2:B:377:MET:HB3 1.93 0.492:E:238:ILE:CD1 2:E:378:LEU:HD21 2.42 0.49





Clashoverlap (Å)

2:F:315:CYS:HB2 2:F:351:PHE:HD1 1.78 0.491:J:317:PHE:CB 1:J:321:MET:CE 2.91 0.491:J:3:GLU:HB3 1:J:62:ARG:NH1 2.27 0.492:B:234:ILE:O 2:B:238:ILE:HG12 2.14 0.48

2:B:315:CYS:HB2 2:B:351:PHE:HD1 1.78 0.481:C:3:GLU:HB3 1:C:62:ARG:NH1 2.28 0.482:G:315:CYS:HB2 2:G:351:PHE:HD1 1.78 0.481:I:3:GLU:HB3 1:I:62:ARG:NH1 2.28 0.48

1:J:173:PRO:HD3 1:J:380:ARG:CZ 2.43 0.481:L:317:PHE:CB 1:L:321:MET:CE 2.91 0.481:L:173:PRO:HD3 1:L:380:ARG:CZ 2.43 0.482:A:238:ILE:CD1 2:A:378:LEU:HD21 2.43 0.482:H:315:CYS:HB2 2:H:351:PHE:HD1 1.78 0.481:L:69:GLU:OE2 2:G:251:ASP:OD2 2.30 0.482:F:238:ILE:CD1 2:F:378:LEU:HD21 2.43 0.482:G:238:ILE:CD1 2:G:378:LEU:HD21 2.43 0.482:H:238:ILE:CD1 2:H:378:LEU:HD21 2.42 0.481:J:344:TRP:HH2 1:J:425:TYR:HB3 1.79 0.481:L:344:TRP:HH2 1:L:425:TYR:HB3 1.78 0.482:B:238:ILE:CD1 2:B:378:LEU:HD21 2.42 0.482:H:234:ILE:O 2:H:238:ILE:HG12 2.14 0.481:I:32:PRO:HB3 1:I:81:PHE:CD1 2.49 0.481:J:32:PRO:HB3 1:J:81:PHE:CD1 2.49 0.481:K:69:GLU:OE2 2:H:251:ASP:OD2 2.30 0.481:C:32:PRO:HB3 1:C:81:PHE:CD1 2.49 0.481:D:344:TRP:HH2 1:D:425:TYR:HB3 1.78 0.481:I:173:PRO:HD3 1:I:380:ARG:CZ 2.43 0.481:I:323:MET:SD 2:A:224:TYR:CE2 3.06 0.481:K:173:PRO:HD3 1:K:380:ARG:CZ 2.43 0.481:L:32:PRO:HB3 1:L:81:PHE:CD1 2.49 0.481:C:173:PRO:HD3 1:C:380:ARG:CZ 2.43 0.481:D:173:PRO:HD3 1:D:380:ARG:CZ 2.43 0.482:B:238:ILE:HD11 2:B:378:LEU:HD21 1.96 0.482:H:238:ILE:HD11 2:H:378:LEU:HD21 1.96 0.481:J:173:PRO:HD3 1:J:380:ARG:NH2 2.29 0.481:K:344:TRP:HH2 1:K:425:TYR:HB3 1.79 0.481:L:173:PRO:HD3 1:L:380:ARG:NH2 2.29 0.482:E:224:TYR:CE2 1:C:323:MET:SD 3.07 0.482:E:238:ILE:HD11 2:E:378:LEU:HD21 1.96 0.482:B:305:CYS:O 2:B:306:ASP:HB2 2.13 0.482:A:234:ILE:O 2:A:238:ILE:HG12 2.14 0.48





Clashoverlap (Å)

2:A:238:ILE:HD11 2:A:378:LEU:HD21 1.96 0.482:H:305:CYS:O 2:H:306:ASP:HB2 2.14 0.481:J:37:VAL:O 1:J:37:VAL:HG12 2.14 0.48

1:L:37:VAL:HG12 1:L:37:VAL:O 2.14 0.481:D:32:PRO:HB3 1:D:81:PHE:CD1 2.49 0.472:E:234:ILE:O 2:E:238:ILE:HG12 2.14 0.472:F:234:ILE:O 2:F:238:ILE:HG12 2.14 0.472:G:234:ILE:O 2:G:238:ILE:HG12 2.14 0.472:A:305:CYS:O 2:A:306:ASP:HB2 2.13 0.471:D:37:VAL:O 1:D:37:VAL:HG12 2.14 0.47

2:G:238:ILE:HD11 2:G:378:LEU:HD21 1.96 0.471:K:32:PRO:HB3 1:K:81:PHE:CD1 2.49 0.471:I:69:GLU:OE2 2:E:251:ASP:OD2 2.31 0.472:E:305:CYS:O 2:E:306:ASP:HB2 2.14 0.47

2:F:238:ILE:HD11 2:F:378:LEU:HD21 1.96 0.472:F:305:CYS:O 2:F:306:ASP:HB2 2.13 0.472:G:145:THR:HB 5:G:501:GTP:O1B 2.14 0.471:I:344:TRP:HH2 1:I:425:TYR:HB3 1.79 0.471:K:37:VAL:O 1:K:37:VAL:HG12 2.14 0.47

2:E:103:TYR:CE2 2:E:148:GLY:HA2 2.49 0.472:G:305:CYS:O 2:G:306:ASP:HB2 2.13 0.47

2:A:103:TYR:CE2 2:A:148:GLY:HA2 2.49 0.471:C:344:TRP:HH2 1:C:425:TYR:HB3 1.79 0.471:I:173:PRO:HD3 1:I:380:ARG:NH2 2.30 0.471:C:173:PRO:HD3 1:C:380:ARG:NH2 2.30 0.472:B:103:TYR:CE2 2:B:148:GLY:HA2 2.49 0.471:D:173:PRO:HD3 1:D:380:ARG:NH2 2.29 0.471:K:173:PRO:HD3 1:K:380:ARG:NH2 2.29 0.472:F:103:TYR:CE2 2:F:148:GLY:HA2 2.49 0.472:G:103:TYR:CE2 2:G:148:GLY:HA2 2.49 0.472:H:103:TYR:CE2 2:H:148:GLY:HA2 2.49 0.472:B:67:PHE:HB2 2:B:92:LEU:HD23 1.96 0.472:G:67:PHE:HB2 2:G:92:LEU:HD23 1.96 0.472:H:67:PHE:HB2 2:H:92:LEU:HD23 1.96 0.472:F:67:PHE:HB2 2:F:92:LEU:HD23 1.97 0.471:I:330:MET:HG3 1:I:349:VAL:HG11 1.96 0.472:F:224:TYR:CE2 1:L:323:MET:SD 3.08 0.471:K:330:MET:HG3 1:K:349:VAL:HG11 1.96 0.471:L:330:MET:HG3 1:L:349:VAL:HG11 1.96 0.472:A:3:GLU:HB2 2:A:129:CYS:SG 2.55 0.462:A:67:PHE:HB2 2:A:92:LEU:HD23 1.96 0.46





Clashoverlap (Å)

1:C:330:MET:HG3 1:C:349:VAL:HG11 1.96 0.462:E:3:GLU:HB2 2:E:129:CYS:SG 2.55 0.462:E:67:PHE:HB2 2:E:92:LEU:HD23 1.96 0.461:J:346:PRO:HG3 2:G:394:LYS:CG 2.44 0.46

1:I:37:VAL:O 1:I:37:VAL:HG12 2.14 0.461:C:37:VAL:O 1:C:37:VAL:HG12 2.14 0.462:H:3:GLU:HB2 2:H:129:CYS:SG 2.55 0.462:B:3:GLU:HB2 2:B:129:CYS:SG 2.55 0.46

1:D:330:MET:HG3 1:D:349:VAL:HG11 1.96 0.461:J:330:MET:HG3 1:J:349:VAL:HG11 1.96 0.462:F:241:SER:HG 2:F:250:VAL:H 1.64 0.462:G:241:SER:HG 2:G:250:VAL:H 1.64 0.462:G:3:GLU:HB2 2:G:129:CYS:SG 2.55 0.46

2:A:242:LEU:HD11 2:A:252:LEU:CD1 2.42 0.462:F:3:GLU:HB2 2:F:129:CYS:SG 2.55 0.46

2:H:242:LEU:HD11 2:H:252:LEU:CD1 2.42 0.462:B:242:LEU:HD11 2:B:252:LEU:CD1 2.43 0.462:E:242:LEU:HD11 2:E:252:LEU:CD1 2.42 0.461:C:257:MET:HB3 1:C:266:PHE:CE1 2.52 0.452:G:242:LEU:HD11 2:G:252:LEU:CD1 2.42 0.451:J:257:MET:HB3 1:J:266:PHE:CE1 2.51 0.451:L:257:MET:HB3 1:L:266:PHE:CE1 2.51 0.451:C:44:LEU:HD12 1:C:47:ILE:HD12 1.98 0.451:I:44:LEU:HD12 1:I:47:ILE:HD12 1.98 0.452:F:242:LEU:HD11 2:F:252:LEU:CD1 2.43 0.452:H:145:THR:HB 5:H:501:GTP:O1B 2.17 0.451:I:257:MET:HB3 1:I:266:PHE:CE1 2.52 0.451:K:350:LYS:HD2 2:B:179:THR:O 2.17 0.451:J:323:MET:SD 2:G:224:TYR:CE2 3.10 0.451:I:49:VAL:HG13 1:I:50:TYR:N 2.32 0.452:A:145:THR:HB 5:A:501:GTP:O1B 2.17 0.451:L:44:LEU:HD12 1:L:47:ILE:HD12 1.97 0.451:C:49:VAL:HG13 1:C:50:TYR:N 2.32 0.452:H:224:TYR:CE2 1:D:323:MET:SD 3.10 0.452:E:145:THR:HB 5:E:501:GTP:O1B 2.17 0.451:I:175:VAL:HG12 2:E:329:ASN:OD1 2.17 0.451:J:44:LEU:HD12 1:J:47:ILE:HD12 1.98 0.452:B:269:LEU:N 2:B:269:LEU:HD12 2.32 0.44

2:F:269:LEU:HD12 2:F:269:LEU:N 2.32 0.441:K:267:MET:HE2 1:K:299:MET:HE3 1.99 0.441:K:44:LEU:HD12 1:K:47:ILE:HD12 1.98 0.44





Clashoverlap (Å)

1:D:257:MET:HB3 1:D:266:PHE:CE1 2.52 0.442:H:269:LEU:HD12 2:H:269:LEU:N 2.32 0.441:K:257:MET:HB3 1:K:266:PHE:CE1 2.52 0.442:A:15:GLN:O 2:A:18:ASN:HB2 2.18 0.44

1:K:323:MET:SD 2:B:224:TYR:CE2 3.11 0.442:E:15:GLN:O 2:E:18:ASN:HB2 2.18 0.44

1:K:49:VAL:HG13 1:K:50:TYR:N 2.33 0.442:A:269:LEU:N 2:A:269:LEU:HD12 2.32 0.44

1:D:44:LEU:HD12 1:D:47:ILE:HD12 1.98 0.441:D:49:VAL:HG13 1:D:50:TYR:N 2.33 0.442:G:269:LEU:HD12 2:G:269:LEU:N 2.33 0.441:L:175:VAL:HG12 2:G:329:ASN:OD1 2.18 0.44

2:B:15:GLN:O 2:B:18:ASN:HB2 2.18 0.442:E:172:TYR:OH 2:E:387:ALA:HB1 2.18 0.442:F:145:THR:HB 5:F:501:GTP:O1B 2.17 0.442:F:54:SER:CB 2:F:128:GLN:OE1 2.66 0.442:G:54:SER:CB 2:G:128:GLN:OE1 2.66 0.442:H:15:GLN:O 2:H:18:ASN:HB2 2.18 0.44

1:K:175:VAL:HG12 2:H:329:ASN:OD1 2.17 0.441:C:317:PHE:CB 1:C:321:MET:HE1 2.41 0.442:E:269:LEU:N 2:E:269:LEU:HD12 2.32 0.442:A:54:SER:CB 2:A:128:GLN:OE1 2.66 0.432:A:172:TYR:OH 2:A:387:ALA:HB1 2.18 0.431:I:317:PHE:CB 1:I:321:MET:HE1 2.41 0.43

1:C:267:MET:HE2 1:C:299:MET:HE3 2.00 0.431:C:3:GLU:OE2 1:C:127:CYS:HB2 2.18 0.432:E:54:SER:CB 2:E:128:GLN:OE1 2.66 0.432:F:15:GLN:O 2:F:18:ASN:HB2 2.18 0.432:H:54:SER:CB 2:H:128:GLN:OE1 2.66 0.431:I:3:GLU:OE2 1:I:127:CYS:HB2 2.18 0.43

1:J:49:VAL:HG13 1:J:50:TYR:N 2.33 0.431:K:3:GLU:OE2 1:K:127:CYS:HB2 2.18 0.431:L:49:VAL:HG13 1:L:50:TYR:N 2.33 0.432:A:181:VAL:HG11 2:A:404:PHE:CZ 2.53 0.432:B:54:SER:CB 2:B:128:GLN:OE1 2.66 0.431:C:80:ALA:O 1:C:81:PHE:CB 2.67 0.431:D:3:GLU:OE2 1:D:127:CYS:HB2 2.18 0.43

2:F:181:VAL:HG11 2:F:404:PHE:CZ 2.54 0.431:I:80:ALA:O 1:I:81:PHE:CB 2.67 0.43

2:B:145:THR:HB 5:B:501:GTP:O1B 2.19 0.432:G:15:GLN:O 2:G:18:ASN:HB2 2.18 0.43





Clashoverlap (Å)

1:K:80:ALA:O 1:K:81:PHE:CB 2.67 0.432:A:180:ALA:HB3 2:A:183:GLU:HG3 2.00 0.431:D:80:ALA:O 1:D:81:PHE:CB 2.67 0.43

2:E:180:ALA:HB3 2:E:183:GLU:HG3 2.00 0.432:G:181:VAL:HG11 2:G:404:PHE:CZ 2.54 0.432:B:115:ILE:HD11 2:B:156:ARG:HG3 1.99 0.432:B:180:ALA:HB3 2:B:183:GLU:HG3 2.00 0.432:E:181:VAL:HG11 2:E:404:PHE:CZ 2.53 0.432:H:115:ILE:HD11 2:H:156:ARG:HG3 1.99 0.432:H:180:ALA:HB3 2:H:183:GLU:HG3 2.00 0.432:H:332:ILE:HG23 2:H:351:PHE:HD2 1.82 0.432:H:172:TYR:OH 2:H:387:ALA:HB1 2.18 0.432:B:182:VAL:O 2:B:182:VAL:HG22 2.19 0.43

2:B:181:VAL:HG11 2:B:404:PHE:CZ 2.53 0.432:B:332:ILE:HG23 2:B:351:PHE:HD2 1.82 0.432:B:172:TYR:OH 2:B:387:ALA:HB1 2.18 0.432:H:181:VAL:HG11 2:H:404:PHE:CZ 2.53 0.432:F:172:TYR:OH 2:F:387:ALA:HB1 2.18 0.432:G:172:TYR:OH 2:G:387:ALA:HB1 2.18 0.432:H:182:VAL:O 2:H:182:VAL:HG22 2.19 0.431:J:80:ALA:O 1:J:81:PHE:CB 2.67 0.431:L:80:ALA:O 1:L:81:PHE:CB 2.67 0.43

2:A:184:PRO:HG3 2:A:394:LYS:CE 2.49 0.431:D:267:MET:HE2 1:D:299:MET:HE3 2.01 0.432:H:283:HIS:HB2 2:E:88:HIS:HB3 2.00 0.432:G:115:ILE:HD11 2:G:156:ARG:HG3 1.99 0.432:G:332:ILE:HG23 2:G:351:PHE:HD2 1.82 0.432:F:179:THR:O 1:L:350:LYS:HD2 2.19 0.431:L:3:GLU:OE2 1:L:127:CYS:HB2 2.18 0.43

2:A:115:ILE:HD11 2:A:156:ARG:HG3 1.99 0.422:E:184:PRO:HG3 2:E:394:LYS:CE 2.49 0.422:F:115:ILE:HD11 2:F:156:ARG:HG3 1.99 0.422:F:332:ILE:HG23 2:F:351:PHE:HD2 1.82 0.422:H:184:PRO:HG3 2:H:394:LYS:CE 2.49 0.421:I:267:MET:HE2 1:I:299:MET:HE3 2.01 0.421:J:3:GLU:OE2 1:J:127:CYS:HB2 2.18 0.422:B:3:GLU:HG2 2:B:51:THR:HA 2.02 0.422:E:210:TYR:CE1 1:C:324:LYS:HB2 2.54 0.422:F:180:ALA:HB3 2:F:183:GLU:HG3 2.00 0.422:G:180:ALA:HB3 2:G:183:GLU:HG3 2.00 0.422:H:3:GLU:HG2 2:H:51:THR:HA 2.02 0.42





Clashoverlap (Å)

2:H:88:HIS:HB3 2:G:283:HIS:HB3 1.99 0.422:B:184:PRO:HG3 2:B:394:LYS:CE 2.49 0.422:E:3:GLU:HG2 2:E:51:THR:HA 2.01 0.422:F:182:VAL:O 2:F:182:VAL:HG22 2.19 0.42

2:G:182:VAL:HG22 2:G:182:VAL:O 2.19 0.422:F:184:PRO:HG3 2:F:394:LYS:CE 2.49 0.422:G:184:PRO:HG3 2:G:394:LYS:CE 2.49 0.422:G:3:GLU:HG2 2:G:51:THR:HA 2.02 0.422:A:3:GLU:HG2 2:A:51:THR:HA 2.02 0.422:E:115:ILE:HD11 2:E:156:ARG:HG3 2.00 0.422:H:283:HIS:HB3 2:E:88:HIS:HB3 2.00 0.422:F:3:GLU:HG2 2:F:51:THR:HA 2.02 0.422:H:295:CYS:HB3 2:H:377:MET:HE2 2.01 0.422:F:283:HIS:HB3 2:B:88:HIS:HB3 2.00 0.422:H:177:VAL:O 2:H:177:VAL:HG12 2.19 0.421:I:324:LYS:HB2 2:A:210:TYR:CE1 2.55 0.422:A:88:HIS:HB3 2:B:283:HIS:HB3 2.00 0.42

2:B:177:VAL:HG12 2:B:177:VAL:O 2.20 0.422:B:295:CYS:HB3 2:B:377:MET:HE2 2.02 0.422:H:179:THR:O 1:D:350:LYS:HD2 2.20 0.42

1:J:267:MET:HE1 1:J:299:MET:HE2 2.02 0.422:A:177:VAL:HG12 2:A:177:VAL:O 2.19 0.422:A:182:VAL:O 2:A:182:VAL:HG22 2.19 0.42

2:A:269:LEU:HD23 2:A:303:VAL:HB 2.01 0.422:B:269:LEU:HD23 2:B:303:VAL:HB 2.01 0.422:F:295:CYS:HB3 2:F:377:MET:HE2 2.02 0.422:G:295:CYS:HB3 2:G:377:MET:HE2 2.02 0.422:E:179:THR:O 1:C:350:LYS:HD2 2.20 0.421:D:317:PHE:CB 1:D:321:MET:HE1 2.43 0.421:D:344:TRP:NE1 1:D:345:ILE:HG13 2.35 0.422:E:269:LEU:HD23 2:E:303:VAL:HB 2.01 0.422:H:265:ILE:HG23 2:H:432:TYR:CE2 2.55 0.421:K:344:TRP:NE1 1:K:345:ILE:HG13 2.35 0.421:L:344:TRP:NE1 1:L:345:ILE:HG13 2.35 0.421:D:52:ASN:HB2 1:D:60:VAL:HG23 2.02 0.412:E:177:VAL:O 2:E:177:VAL:HG12 2.20 0.412:E:182:VAL:O 2:E:182:VAL:HG22 2.19 0.41

2:H:269:LEU:HD23 2:H:303:VAL:HB 2.01 0.411:K:317:PHE:CB 1:K:321:MET:HE1 2.43 0.411:C:344:TRP:NE1 1:C:345:ILE:HG13 2.35 0.412:G:269:LEU:HD23 2:G:303:VAL:HB 2.01 0.41





Clashoverlap (Å)

1:K:322:SER:HB2 2:B:221:ARG:HB2 2.01 0.412:A:332:ILE:HG23 2:A:351:PHE:HD2 1.82 0.412:B:265:ILE:HG23 2:B:432:TYR:CE2 2.55 0.411:C:52:ASN:HB2 1:C:60:VAL:HG23 2.02 0.411:J:313:VAL:HG13 1:J:349:VAL:HA 2.02 0.411:J:52:ASN:HB2 1:J:60:VAL:HG23 2.02 0.41

1:L:313:VAL:HG13 1:L:349:VAL:HA 2.02 0.412:A:88:HIS:HB3 2:B:283:HIS:HB2 2.02 0.41

1:C:257:MET:HB3 1:C:266:PHE:HE1 1.85 0.412:E:265:ILE:HG23 2:E:432:TYR:CE2 2.55 0.412:E:332:ILE:HG23 2:E:351:PHE:HD2 1.82 0.411:I:52:ASN:HB2 1:I:60:VAL:HG23 2.02 0.411:J:344:TRP:NE1 1:J:345:ILE:HG13 2.35 0.411:K:52:ASN:HB2 1:K:60:VAL:HG23 2.02 0.411:I:323:MET:CE 2:A:179:THR:HG21 2.51 0.412:A:265:ILE:HG23 2:A:432:TYR:CE2 2.55 0.412:F:269:LEU:HD23 2:F:303:VAL:HB 2.01 0.411:J:323:MET:CE 2:G:179:THR:HG21 2.50 0.411:I:344:TRP:NE1 1:I:345:ILE:HG13 2.35 0.411:L:52:ASN:HB2 1:L:60:VAL:HG23 2.02 0.41

1:D:313:VAL:HG13 1:D:349:VAL:HA 2.02 0.411:J:257:MET:HB3 1:J:266:PHE:HE1 1.85 0.411:J:317:PHE:CB 1:J:321:MET:HE1 2.43 0.411:L:257:MET:HB3 1:L:266:PHE:HE1 1.85 0.411:L:317:PHE:CB 1:L:321:MET:HE1 2.43 0.412:G:265:ILE:HG23 2:G:432:TYR:CE2 2.55 0.411:I:257:MET:HB3 1:I:266:PHE:HE1 1.85 0.411:K:313:VAL:HG13 1:K:349:VAL:HA 2.02 0.412:F:265:ILE:HG23 2:F:432:TYR:CE2 2.55 0.411:L:267:MET:HE1 1:L:299:MET:HE2 2.03 0.412:H:32:PRO:O 2:H:86:LEU:CD2 2.69 0.41

2:F:210:TYR:CE1 1:L:324:LYS:HB2 2.56 0.412:A:217:LEU:CD2 2:A:219:ILE:HD12 2.51 0.412:B:32:PRO:O 2:B:86:LEU:CD2 2.69 0.412:E:32:PRO:O 2:E:86:LEU:CD2 2.69 0.41

2:F:177:VAL:HG12 2:F:177:VAL:O 2.20 0.412:F:32:PRO:O 2:F:86:LEU:CD2 2.69 0.412:G:177:VAL:O 2:G:177:VAL:HG12 2.20 0.412:G:32:PRO:O 2:G:86:LEU:CD2 2.69 0.411:J:143:THR:O 1:J:147:MET:HG3 2.21 0.41

1:K:257:MET:HB3 1:K:266:PHE:HE1 1.85 0.41Continued on next page...




Clashoverlap (Å)

1:L:143:THR:O 1:L:147:MET:HG3 2.21 0.411:C:313:VAL:HG13 1:C:349:VAL:HA 2.02 0.401:D:257:MET:HB3 1:D:266:PHE:HE1 1.85 0.402:E:217:LEU:CD2 2:E:219:ILE:HD12 2.52 0.401:I:350:LYS:HD2 2:A:179:THR:O 2.21 0.402:A:32:PRO:O 2:A:86:LEU:CD2 2.69 0.40

1:I:313:VAL:HG13 1:I:349:VAL:HA 2.02 0.401:D:143:THR:O 1:D:147:MET:HG3 2.21 0.402:F:283:HIS:HB2 2:B:88:HIS:HB3 2.03 0.401:J:350:LYS:HD2 2:G:179:THR:O 2.21 0.401:K:143:THR:O 1:K:147:MET:HG3 2.21 0.40

2:G:217:LEU:CD2 2:G:219:ILE:HD12 2.51 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 C 424/426 (100%) 408 (96%) 15 (4%) 1 (0%) 47 79

1 D 424/426 (100%) 408 (96%) 15 (4%) 1 (0%) 47 79

1 I 424/426 (100%) 408 (96%) 15 (4%) 1 (0%) 47 79

1 J 424/426 (100%) 408 (96%) 15 (4%) 1 (0%) 47 79

1 K 424/426 (100%) 408 (96%) 15 (4%) 1 (0%) 47 79

1 L 424/426 (100%) 408 (96%) 15 (4%) 1 (0%) 47 79

2 A 424/437 (97%) 404 (95%) 20 (5%) 0 100 100

2 B 424/437 (97%) 404 (95%) 20 (5%) 0 100 100

2 E 424/437 (97%) 404 (95%) 20 (5%) 0 100 100

2 F 424/437 (97%) 404 (95%) 20 (5%) 0 100 100Continued on next page...

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#torsion_angles

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#protein_backbone


Continued from previous page...Mol Chain Analysed Favoured Allowed Outliers Percentiles

2 G 424/437 (97%) 404 (95%) 20 (5%) 0 100 100

2 H 424/437 (97%) 404 (95%) 20 (5%) 0 100 100

All All 5088/5178 (98%) 4872 (96%) 210 (4%) 6 (0%) 54 84

All (6) Ramachandran outliers are listed below:

Mol Chain Res Type1 K 339 SER1 I 339 SER1 J 339 SER1 C 339 SER1 D 339 SER1 L 339 SER

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 C 365/367 (100%) 362 (99%) 3 (1%) 81 89

1 D 365/367 (100%) 362 (99%) 3 (1%) 81 89

1 I 365/367 (100%) 362 (99%) 3 (1%) 81 89

1 J 365/367 (100%) 362 (99%) 3 (1%) 81 89

1 K 365/367 (100%) 362 (99%) 3 (1%) 81 89

1 L 365/367 (100%) 362 (99%) 3 (1%) 81 89

2 A 357/367 (97%) 351 (98%) 6 (2%) 60 78

2 B 357/367 (97%) 351 (98%) 6 (2%) 60 78

2 E 357/367 (97%) 351 (98%) 6 (2%) 60 78

2 F 357/367 (97%) 351 (98%) 6 (2%) 60 78

2 G 357/367 (97%) 351 (98%) 6 (2%) 60 78

2 H 357/367 (97%) 351 (98%) 6 (2%) 60 78

All All 4332/4404 (98%) 4278 (99%) 54 (1%) 72 84

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#protein_sidechains


All (54) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 K 77 ARG1 K 159 TYR1 K 222 TYR2 H 86 LEU2 H 132 LEU2 H 192 HIS2 H 195 LEU2 H 224 TYR2 H 433 GLU1 I 77 ARG1 I 159 TYR1 I 222 TYR2 E 86 LEU2 E 132 LEU2 E 192 HIS2 E 195 LEU2 E 224 TYR2 E 433 GLU1 J 77 ARG1 J 159 TYR1 J 222 TYR1 C 77 ARG1 C 159 TYR1 C 222 TYR1 D 77 ARG1 D 159 TYR1 D 222 TYR2 F 86 LEU2 F 132 LEU2 F 192 HIS2 F 195 LEU2 F 224 TYR2 F 433 GLU2 A 86 LEU2 A 132 LEU2 A 192 HIS2 A 195 LEU2 A 224 TYR2 A 433 GLU2 B 86 LEU2 B 132 LEU2 B 192 HIS



Continued from previous page...Mol Chain Res Type2 B 195 LEU2 B 224 TYR2 B 433 GLU1 L 77 ARG1 L 159 TYR1 L 222 TYR2 G 86 LEU2 G 132 LEU2 G 192 HIS2 G 195 LEU2 G 224 TYR2 G 433 GLU

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (30)such sidechains are listed below:

Mol Chain Res Type1 K 256 ASN1 K 347 ASN1 K 396 HIS2 H 31 GLN2 H 228 ASN1 I 256 ASN1 I 347 ASN1 I 396 HIS2 E 31 GLN2 E 228 ASN1 J 256 ASN1 J 347 ASN1 J 396 HIS1 C 256 ASN1 C 347 ASN1 C 396 HIS1 D 256 ASN1 D 347 ASN1 D 396 HIS2 F 31 GLN2 F 228 ASN2 A 31 GLN2 A 228 ASN2 B 31 GLN2 B 228 ASN1 L 256 ASN



Continued from previous page...Mol Chain Res Type1 L 347 ASN1 L 396 HIS2 G 31 GLN2 G 228 ASN

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○

Of 24 ligands modelled in this entry, 12 are monoatomic - leaving 12 for Mogul analysis.

In the following table, the Counts columns list the number of bonds (or angles) for which Mogulstatistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are defined in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bondlength (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

Mol Type Chain Res Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

5 GTP E 501 4 26,34,34 1.44 3 (11%) 33,54,54 2.12 9 (27%)5 GTP G 501 4 26,34,34 1.43 3 (11%) 33,54,54 2.10 9 (27%)3 G2P K 501 4 26,34,34 2.76 8 (30%) 30,54,54 1.35 4 (13%)3 G2P J 501 4 26,34,34 2.75 8 (30%) 30,54,54 1.31 3 (10%)5 GTP H 501 4 26,34,34 1.43 3 (11%) 33,54,54 2.09 9 (27%)3 G2P C 501 4 26,34,34 2.77 7 (26%) 30,54,54 1.37 4 (13%)3 G2P L 501 4 26,34,34 2.77 8 (30%) 30,54,54 1.33 4 (13%)5 GTP F 501 4 26,34,34 1.44 3 (11%) 33,54,54 2.05 9 (27%)

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#rna

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#nonstandard_residues_and_ligands




Mol Type Chain Res Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

5 GTP B 501 4 26,34,34 1.46 3 (11%) 33,54,54 2.10 8 (24%)3 G2P I 501 4 26,34,34 2.80 8 (30%) 30,54,54 1.40 4 (13%)5 GTP A 501 4 26,34,34 1.45 3 (11%) 33,54,54 2.12 8 (24%)3 G2P D 501 4 26,34,34 2.75 9 (34%) 30,54,54 1.33 4 (13%)

In the following table, the Chirals column lists the number of chiral outliers, the number of chiralcenters analysed, the number of these observed in the model and the number defined in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.’-’ means no outliers of that kind were identified.

Mol Type Chain Res Link Chirals Torsions Rings5 GTP E 501 4 - 4/18/38/38 0/3/3/35 GTP G 501 4 - 4/18/38/38 0/3/3/33 G2P K 501 4 - 5/18/38/38 0/3/3/33 G2P J 501 4 - 6/18/38/38 0/3/3/35 GTP H 501 4 - 4/18/38/38 0/3/3/33 G2P C 501 4 - 4/18/38/38 0/3/3/33 G2P L 501 4 - 6/18/38/38 0/3/3/35 GTP F 501 4 - 4/18/38/38 0/3/3/35 GTP B 501 4 - 4/18/38/38 0/3/3/33 G2P I 501 4 - 5/18/38/38 0/3/3/35 GTP A 501 4 - 4/18/38/38 0/3/3/33 G2P D 501 4 - 6/18/38/38 0/3/3/3

All (66) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)3 I 501 G2P C4-N9 -10.61 1.33 1.473 C 501 G2P C4-N9 -10.48 1.33 1.473 K 501 G2P C4-N9 -10.40 1.33 1.473 D 501 G2P C4-N9 -10.36 1.33 1.473 L 501 G2P C4-N9 -10.32 1.34 1.473 J 501 G2P C4-N9 -10.28 1.34 1.475 B 501 GTP C6-C5 5.69 1.51 1.415 G 501 GTP C6-C5 5.64 1.51 1.415 A 501 GTP C6-C5 5.64 1.51 1.415 F 501 GTP C6-C5 5.63 1.51 1.415 H 501 GTP C6-C5 5.56 1.50 1.415 E 501 GTP C6-C5 5.54 1.50 1.41



Continued from previous page...Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)3 C 501 G2P PA-O2A 4.25 1.61 1.513 L 501 G2P PA-O2A 4.25 1.61 1.513 I 501 G2P PA-O2A 4.23 1.61 1.513 J 501 G2P PA-O2A 4.23 1.61 1.513 D 501 G2P PA-O2A 4.22 1.61 1.513 K 501 G2P PA-O2A 4.20 1.61 1.513 D 501 G2P PB-O2B 4.04 1.61 1.513 K 501 G2P PB-O2B 4.02 1.61 1.513 C 501 G2P PB-O2B 4.01 1.61 1.513 L 501 G2P PB-O2B 4.01 1.61 1.513 J 501 G2P PB-O2B 4.01 1.61 1.513 I 501 G2P PB-O2B 3.96 1.61 1.513 I 501 G2P PB-O1B -3.44 1.48 1.563 J 501 G2P PB-O1B -3.43 1.48 1.563 K 501 G2P PB-O1B -3.43 1.48 1.563 C 501 G2P PB-O1B -3.42 1.48 1.563 L 501 G2P PA-O1A -3.41 1.48 1.563 L 501 G2P PB-O1B -3.41 1.48 1.563 I 501 G2P PA-O1A -3.41 1.48 1.563 J 501 G2P PA-O1A -3.41 1.48 1.563 D 501 G2P PA-O1A -3.40 1.48 1.563 D 501 G2P PB-O1B -3.39 1.48 1.563 C 501 G2P PA-O1A -3.38 1.48 1.563 K 501 G2P PA-O1A -3.36 1.48 1.563 I 501 G2P C8-N9 -3.09 1.35 1.453 K 501 G2P C8-N9 -3.08 1.35 1.453 L 501 G2P C8-N9 -3.07 1.35 1.453 C 501 G2P C8-N9 -3.04 1.35 1.453 J 501 G2P C8-N9 -3.03 1.35 1.453 I 501 G2P PA-O5’ 3.03 1.61 1.573 D 501 G2P C8-N9 -3.01 1.35 1.453 L 501 G2P PA-O5’ 3.00 1.61 1.573 J 501 G2P PA-O5’ 2.92 1.61 1.573 C 501 G2P PA-O5’ 2.89 1.61 1.575 H 501 GTP C5-C4 2.80 1.48 1.403 K 501 G2P PA-O5’ 2.80 1.61 1.575 A 501 GTP C5-C4 2.79 1.48 1.405 B 501 GTP C5-C4 2.76 1.48 1.405 G 501 GTP C5-C4 2.76 1.48 1.405 F 501 GTP C5-C4 2.75 1.48 1.403 D 501 G2P PA-O5’ 2.74 1.61 1.575 E 501 GTP C5-C4 2.73 1.48 1.40



Continued from previous page...Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)5 E 501 GTP O4’-C1’ 2.67 1.44 1.415 B 501 GTP O4’-C1’ 2.66 1.44 1.415 A 501 GTP O4’-C1’ 2.63 1.44 1.415 H 501 GTP O4’-C1’ 2.56 1.44 1.415 F 501 GTP O4’-C1’ 2.54 1.44 1.415 G 501 GTP O4’-C1’ 2.44 1.44 1.413 L 501 G2P PB-O3B 2.33 1.61 1.583 K 501 G2P PB-O3B 2.27 1.60 1.583 I 501 G2P PB-O3B 2.18 1.60 1.583 D 501 G2P PB-O3B 2.07 1.60 1.583 J 501 G2P C2-N1 -2.01 1.36 1.443 D 501 G2P C2-N1 -2.01 1.36 1.44

All (75) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 G 501 GTP C2-N3-C4 5.87 122.06 115.365 H 501 GTP C2-N3-C4 5.83 122.02 115.365 B 501 GTP C2-N3-C4 5.75 121.93 115.365 F 501 GTP C2-N3-C4 5.69 121.85 115.365 A 501 GTP C2-N3-C4 5.58 121.73 115.365 E 501 GTP C2-N3-C4 5.51 121.66 115.365 B 501 GTP C4-C5-N7 -4.33 104.89 109.405 E 501 GTP C5-C6-N1 -4.32 117.52 123.435 E 501 GTP C4-C5-N7 -4.29 104.92 109.405 G 501 GTP C4-C5-N7 -4.28 104.94 109.405 A 501 GTP C4-C5-N7 -4.28 104.94 109.405 B 501 GTP C5-C6-N1 -4.25 117.61 123.435 F 501 GTP C4-C5-N7 -4.23 105.00 109.405 A 501 GTP C5-C6-N1 -4.20 117.69 123.435 H 501 GTP C4-C5-N7 -4.11 105.11 109.405 H 501 GTP C5-C6-N1 -4.04 117.91 123.433 C 501 G2P PG-O3B-PB -4.03 118.44 132.625 G 501 GTP C5-C6-N1 -4.00 117.95 123.435 F 501 GTP C5-C6-N1 -4.00 117.96 123.435 E 501 GTP C6-N1-C2 3.97 122.23 115.935 A 501 GTP C6-N1-C2 3.95 122.21 115.933 J 501 G2P PG-O3B-PB -3.92 118.82 132.623 D 501 G2P PG-O3B-PB -3.91 118.86 132.625 B 501 GTP C6-N1-C2 3.90 122.13 115.935 H 501 GTP C6-N1-C2 3.89 122.11 115.933 I 501 G2P PG-O3B-PB -3.87 119.00 132.62



Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 G 501 GTP C6-N1-C2 3.85 122.05 115.935 F 501 GTP C6-N1-C2 3.75 121.89 115.933 K 501 G2P PG-O3B-PB -3.74 119.43 132.625 E 501 GTP PB-O3B-PG -3.70 120.11 132.833 L 501 G2P PG-O3B-PB -3.69 119.62 132.625 A 501 GTP PB-O3B-PG -3.67 120.24 132.833 I 501 G2P O6-C6-N1 -3.51 117.98 122.695 B 501 GTP PB-O3B-PG -3.41 121.13 132.833 K 501 G2P O6-C6-N1 -3.40 118.12 122.693 L 501 G2P O6-C6-N1 -3.35 118.19 122.695 H 501 GTP PB-O3B-PG -3.32 121.44 132.835 F 501 GTP PB-O3B-PG -3.31 121.45 132.835 G 501 GTP PB-O3B-PG -3.28 121.58 132.835 H 501 GTP C6-C5-C4 -3.25 117.70 120.803 C 501 G2P O6-C6-N1 -3.24 118.33 122.695 G 501 GTP C6-C5-C4 -3.22 117.73 120.803 D 501 G2P O6-C6-N1 -3.20 118.39 122.695 G 501 GTP N3-C2-N1 -3.19 122.97 127.225 A 501 GTP N3-C2-N1 -3.19 122.97 127.225 H 501 GTP N3-C2-N1 -3.18 122.98 127.225 E 501 GTP N3-C2-N1 -3.18 122.98 127.225 F 501 GTP C6-C5-C4 -3.17 117.78 120.805 B 501 GTP N3-C2-N1 -3.15 123.02 127.223 J 501 G2P O6-C6-N1 -3.09 118.54 122.695 A 501 GTP C6-C5-C4 -3.09 117.85 120.805 B 501 GTP C6-C5-C4 -3.02 117.91 120.805 F 501 GTP N3-C2-N1 -3.01 123.21 127.225 E 501 GTP C6-C5-C4 -2.85 118.07 120.803 C 501 G2P C3’-C2’-C1’ 2.79 106.72 101.433 K 501 G2P C3’-C2’-C1’ 2.69 106.55 101.433 I 501 G2P C3’-C2’-C1’ 2.64 106.45 101.433 D 501 G2P C3’-C2’-C1’ 2.63 106.43 101.435 G 501 GTP C3’-C2’-C1’ 2.53 104.78 100.983 L 501 G2P C3’-C2’-C1’ 2.52 106.21 101.433 I 501 G2P O6-C6-C5 2.50 124.96 119.863 J 501 G2P C3’-C2’-C1’ 2.49 106.16 101.435 E 501 GTP O3G-PG-O2G 2.42 116.90 107.645 A 501 GTP O3G-PG-O2G 2.41 116.86 107.645 G 501 GTP O3G-PG-O2G 2.38 116.73 107.643 K 501 G2P O6-C6-C5 2.35 124.66 119.865 H 501 GTP C3’-C2’-C1’ 2.35 104.52 100.985 F 501 GTP O3G-PG-O2G 2.35 116.62 107.64



Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 H 501 GTP O3G-PG-O2G 2.33 116.55 107.645 B 501 GTP O3G-PG-O2G 2.32 116.49 107.643 C 501 G2P O6-C6-C5 2.24 124.42 119.863 L 501 G2P O6-C6-C5 2.20 124.36 119.865 E 501 GTP O4’-C1’-C2’ -2.20 103.71 106.933 D 501 G2P O6-C6-C5 2.15 124.25 119.865 F 501 GTP C3’-C2’-C1’ 2.03 104.03 100.98

There are no chirality outliers.

All (56) torsion outliers are listed below:

Mol Chain Res Type Atoms5 E 501 GTP C5’-O5’-PA-O3A3 C 501 G2P O4’-C4’-C5’-O5’3 C 501 G2P C3’-C4’-C5’-O5’3 C 501 G2P C2’-C1’-N9-C43 L 501 G2P PB-C3A-PA-O1A3 L 501 G2P PB-C3A-PA-O2A3 L 501 G2P O4’-C4’-C5’-O5’3 L 501 G2P C3’-C4’-C5’-O5’3 L 501 G2P C2’-C1’-N9-C43 K 501 G2P O4’-C4’-C5’-O5’3 K 501 G2P C3’-C4’-C5’-O5’3 K 501 G2P C2’-C1’-N9-C45 B 501 GTP C5’-O5’-PA-O1A3 J 501 G2P PB-C3A-PA-O1A3 J 501 G2P O4’-C4’-C5’-O5’3 J 501 G2P C3’-C4’-C5’-O5’3 J 501 G2P C2’-C1’-N9-C45 H 501 GTP C5’-O5’-PA-O1A3 I 501 G2P O4’-C4’-C5’-O5’3 I 501 G2P C3’-C4’-C5’-O5’3 I 501 G2P C2’-C1’-N9-C45 G 501 GTP C5’-O5’-PA-O1A5 A 501 GTP C5’-O5’-PA-O1A5 F 501 GTP C5’-O5’-PA-O1A3 D 501 G2P PB-C3A-PA-O1A3 D 501 G2P O4’-C4’-C5’-O5’3 D 501 G2P C3’-C4’-C5’-O5’3 D 501 G2P C2’-C1’-N9-C43 L 501 G2P C5’-O5’-PA-C3A5 E 501 GTP C4’-C5’-O5’-PA



Continued from previous page...Mol Chain Res Type Atoms5 G 501 GTP C4’-C5’-O5’-PA5 A 501 GTP C4’-C5’-O5’-PA5 F 501 GTP C4’-C5’-O5’-PA5 B 501 GTP C4’-C5’-O5’-PA5 H 501 GTP C4’-C5’-O5’-PA3 J 501 G2P C5’-O5’-PA-C3A5 E 501 GTP C5’-O5’-PA-O1A3 C 501 G2P PB-C3A-PA-O1A3 K 501 G2P PB-C3A-PA-O1A3 I 501 G2P PB-C3A-PA-O1A5 E 501 GTP PA-O3A-PB-O2B5 B 501 GTP PA-O3A-PB-O2B5 H 501 GTP PA-O3A-PB-O2B5 G 501 GTP PA-O3A-PB-O2B5 A 501 GTP PA-O3A-PB-O2B5 F 501 GTP PA-O3A-PB-O2B3 K 501 G2P C5’-O5’-PA-C3A3 D 501 G2P C5’-O5’-PA-C3A3 J 501 G2P PB-C3A-PA-O2A3 D 501 G2P PB-C3A-PA-O2A5 G 501 GTP C5’-O5’-PA-O3A5 A 501 GTP C5’-O5’-PA-O3A5 B 501 GTP PA-O3A-PB-O1B5 H 501 GTP PA-O3A-PB-O1B5 F 501 GTP PA-O3A-PB-O1B3 I 501 G2P C5’-O5’-PA-C3A

There are no ring outliers.

6 monomers are involved in 6 short contacts:

Mol Chain Res Type Clashes Symm-Clashes5 E 501 GTP 1 05 G 501 GTP 1 05 H 501 GTP 1 05 F 501 GTP 1 05 B 501 GTP 1 05 A 501 GTP 1 0

The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. Inaddition, ligands with molecular weight > 250 and outliers as shown on the validation Tables willalso be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles is


within 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier.Any bond that is central to one or more torsion angles identified as an outlier by Mogul will behighlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ringin question and similar rings identified by Mogul is calculated over all ring torsion angles. If theaverage RMSD is greater than 60 degrees and the minimal RMSD between the ring in question andany Mogul-identified rings is also greater than 60 degrees, then that ring is considered an outlier.The outliers are highlighted in purple. The color gray indicates Mogul did not find sufficientequivalents in the CSD to analyse the geometry.

Ligand GTP E 501

Bond lengths Bond angles

Torsions Rings


Ligand GTP G 501


Torsions Rings

Ligand G2P K 501


Torsions Rings


Ligand G2P J 501


Torsions Rings

Ligand GTP H 501


Torsions Rings


Ligand G2P C 501


Torsions Rings

Ligand G2P L 501


Torsions Rings


Ligand GTP F 501


Torsions Rings

Ligand GTP B 501


Torsions Rings


Ligand G2P I 501


Torsions Rings

Ligand GTP A 501


Torsions Rings


Ligand G2P D 501


Torsions Rings

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.


https://www.wwpdb.org/validation/2017/EMValidationReportHelp#polymer_linkage


6 Map visualisation i○

This section contains visualisations of the EMDB entry EMD-8150. 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: 83 Y Index: 40 Z Index: 104

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_visualisation

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#orthogonal_projections

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#central_slices


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: 36 Y Index: 39 Z Index: 117

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 0.043.These images, in conjunction with the slice images, may facilitate assessment of whether an ap-propriate contour level has been provided.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#largest_variance_slices

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#orthogonal_views


6.5 Mask visualisation i○

This section was not generated. No masks/segmentation were deposited.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#masks


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.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_analysis

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_value_distribution


7.2 Volume estimate i○

The volume at the recommended contour level is 202 nm3; this corresponds to an approximatemass of 182 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.

7.3 Rotationally averaged power spectrum i○

This section was not generated. The rotationally averaged power spectrum is only generated forcubic maps.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#volume_estimate

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#raps


8 Fourier-Shell correlation i○

This section was not generated. No FSC curve or half-maps provided.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#fsc_validation


9 Map-model fit i○

This section contains information regarding the fit between EMDB map EMD-8150 and PDBmodel 5JCO. Per-residue inclusion information can be found in section 3 on page 8.

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 0.043at 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.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_fit

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_overlay


9.2 Atom inclusion i○

At the recommended contour level, 75% of all backbone atoms, 57% of all non-hydrogen atoms,are inside the map.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#atom_inclusion_by_contour

Documents

Full wwPDB/EMDataBank EM Map/Model Validation Report · 2018. 2. 24. · m1 r2 e3 c4 i5 q15 n18 p32 m36 p37 ser asp lys thr ile gly gly gly asp d47 t51 s54 p63 r64 f67 l86 f87 h88