Full wwPDB NMR Structure Validation Report iO
May 28, 2020 � 09:59 pm BST
PDB ID : 2GF5Title : Structure of intact FADD (MORT1)
Authors : Carrington, P.E.; Sandu, C.; Wei, Y.; Hill, J.M.; Morisawa, G.; Huang, T.;Gavathiotis, E.; Wei, Y.; Werner, M.H.
Deposited on : 2006-03-21
This is a Full wwPDB NMR Structure Validation Report for a publicly released PDB entry.
We welcome your comments at [email protected]
A user guide is available athttps://www.wwpdb.org/validation/2017/NMRValidationReportHelp
with speci�c help available everywhere you see the iO symbol.
The following versions of software and data (see references iO) were used in the production of this report:
Cyrange : Kirchner and Güntert (2011)NmrClust : Kelley et al. (1996)
MolProbity : 4.02b-467Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)
RCI : v_1n_11_5_13_A (Berjanski et al., 2005)PANAV : Wang et al. (2010)
ShiftChecker : 2.11Ideal geometry (proteins) : Engh & Huber (2001)
Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : 2.11
Page 2 Full wwPDB NMR Structure Validation Report 2GF5
1 Overall quality at a glance iO
The following experimental techniques were used to determine the structure:SOLUTION NMR
The overall completeness of chemical shifts assignment was not calculated.
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.
MetricWhole archive(#Entries)
NMR archive(#Entries)
Clashscore 158937 12864Ramachandran outliers 154571 11451
Sidechain outliers 154315 11428
The table below summarises the geometric issues observed across the polymeric chains and their�t to the experimental data. The red, orange, yellow and green segments indicate the fractionof residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. A cyansegment indicates the fraction of residues that are not part of the well-de�ned cores, and a grey seg-ment represents the fraction of residues that are not modelled. The numeric value for each fractionis indicated below the corresponding segment, with a dot representing fractions <=5%
Mol Chain Length Quality of chain
1 A 191
Page 3 Full wwPDB NMR Structure Validation Report 2GF5
2 Ensemble composition and analysis iO
This entry contains 25 models. Model 22 is the overall representative, medoid model (most similarto other models). The authors have identi�ed model 1 as representative.
The following residues are included in the computation of the global validation metrics.
Well-de�ned (core) protein residuesWell-de�ned core Residue range (total) Backbone RMSD (Å) Medoid model
1 A:2-A:190 (189) 0.80 22
Ill-de�ned regions of proteins are excluded from the global statistics.
Ligands and non-protein polymers are included in the analysis.
The models can be grouped into 7 clusters and 1 single-model cluster was found.
Cluster number Models1 10, 11, 14, 18, 232 5, 7, 8, 203 13, 15, 17, 214 2, 6, 225 1, 19, 246 9, 12, 167 3, 4
Single-model clusters 25
Page 4 Full wwPDB NMR Structure Validation Report 2GF5
3 Entry composition iO
There is only 1 type of molecule in this entry. The entry contains 3036 atoms, of which 1527 arehydrogens and 0 are deuteriums.
� Molecule 1 is a protein called FADD protein.
Mol Chain Residues Atoms Trace
1 A 191Total C H N O S3036 929 1527 282 292 6
0
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceA 1 SER - CLONING ARTIFACT UNP Q13158A 25 TYR PHE ENGINEERED UNP Q13158
Page 5 Full wwPDB NMR Structure Validation Report 2GF5
4 Residue-property plots iO
4.1 Average score per residue in the NMR ensemble
These plots are provided for all protein, RNA and DNA chains in the entry. The �rst graphic is thesame as shown in the summary in section 1 of this report. The second graphic shows the sequencewhere residues are colour-coded according to the number of geometric quality criteria for whichthey contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretchesof 2 or more consecutive residues without any outliers are shown as green connectors. Residueswhich are classi�ed as ill-de�ned in the NMR ensemble, are shown in cyan with an underlinecolour-coded according to the previous scheme. Residues which were present in the experimentalsample, but not modelled in the �nal structure are shown in grey.
• Molecule 1: FADD protein
Chain A:
S1
R30
R34
K35
L36
E37
R38
G42
N53
E56
R64
R71
R72
H73
D74
R77
R78
F101
N102
K110
R113
R114
R117
K120
R132
R135
T138
E139
R140
V141
R142
R146
R166
Q169
M170
R184
R189
S190
G191
4.2 Scores per residue for each member of the ensemble
Colouring as in section 4.1 above.
4.2.1 Score per residue for model 1
• Molecule 1: FADD protein
Chain A:
S1
S16
C27
R30
R34
K35
L36
E37
R38
L49
R64
R71
R72
H73
D74
R77
L97
F101
N102
R117
Q118
I129
R135
T138
E139
R140
R146
E152
K153
H160
R166
M170
R184
N188
R189
S190
G191
4.2.2 Score per residue for model 2
• Molecule 1: FADD protein
Chain A:
S1
D2
S16
R30
K33
R34
K35
L36
E37
R38
G42
N53
H59
T60
E61
L62
R72
R77
R78
V79
D80
A87
F101
N102
R113
R114
L119
K120
I129
R132
Y133
P134
R135
R140
V141
R142
R146
L165
R166
Q169
M170
N171
L172
V173
L186
R189
S190
G191
Page 6 Full wwPDB NMR Structure Validation Report 2GF5
4.2.3 Score per residue for model 3
• Molecule 1: FADD protein
Chain A:
S1
E19
K24
Y25
R30
R34
K35
L36
E37
R38
G42
L43
D44
N53
E56
R64
A68
R71
R72
H73
D74
R77
L97
F101
N102
C105
R114
L119
R140
V141
R142
E154
A164
L165
R166
Q169
R184
G191
4.2.4 Score per residue for model 4
• Molecule 1: FADD protein
Chain A:
S1
R30
K33
R34
K35
L36
E37
R38
V39
Q40
E51
Q52
N53
R64
R71
R72
R77
R78
G89
D96
L97
N102
K110
R114
R117
K120
I126
I129
R132
T138
E139
R140
V141
R142
R146
E152
T157
H160
R166
M170
R184
N188
R189
S190
G191
4.2.5 Score per residue for model 5
• Molecule 1: FADD protein
Chain A:
S1
D2
L15
R30
R34
K35
L36
E37
R38
V39
Q40
L45
Q52
L55
R64
R71
R72
R77
F101
N102
K110
R113
R114
D123
T124
K125
R135
N150
E154
R166
M170
V173
D185
R189
S190
G191
4.2.6 Score per residue for model 6
• Molecule 1: FADD protein
Chain A:
S1
L5
H9
R30
L36
E37
R38
L49
N53
D54
L55
R64
R71
R78
F101
N102
R113
R114
K120
R132
R135
T138
E139
R140
V141
R142
R146
N150
R166
Q169
M170
R189
S190
G191
4.2.7 Score per residue for model 7
• Molecule 1: FADD protein
Chain A:
Page 7 Full wwPDB NMR Structure Validation Report 2GF5
S1
L5
H9
S10
V11
S12
C27
R30
K33
R34
K35
R38
G42
N53
R64
R71
R72
H73
D74
R77
R78
D81
A87
A88
P92
C105
R114
R117
Q118
L119
K120
R132
R135
R140
R146
N150
T151
E152
K153
E154
T157
H160
L165
R166
Q169
M170
R184
Q187
N188
R189
S190
G191
4.2.8 Score per residue for model 8
• Molecule 1: FADD protein
Chain A:
S1
D2
R34
K35
L36
E37
R38
V39
Q40
L43
D44
L45
H59
R64
R71
R77
R78
A90
F101
N102
D111
W112
R113
R114
R117
K120
N136
R140
V141
R142
R146
R166
Q169
M170
Q182
L186
R189
S190
G191
4.2.9 Score per residue for model 9
• Molecule 1: FADD protein
Chain A:
S1
L5
H9
S18
E22
L23
K24
Y25
L26
C27
R30
R34
K35
L36
E56
R64
S69
L70
R71
R72
L97
F101
N102
K110
R113
R114
R117
S122
I126
I129
R132
E139
R140
V141
R142
R146
K153
L165
R166
Q169
M170
R184
G191
4.2.10 Score per residue for model 10
• Molecule 1: FADD protein
Chain A:
S1
D2
S18
Y25
R30
R34
K35
L36
G42
N53
E56
R64
R71
R72
H73
D74
R77
R78
A87
N102
R117
Q118
L119
K120
R132
R135
T138
E139
R140
V141
R142
R166
L172
L186
R189
S190
G191
4.2.11 Score per residue for model 11
• Molecule 1: FADD protein
Chain A:
S1
D2
L5
H9
Y25
R30
K33
L36
L43
E51
E56
P57
G58
R71
R72
H73
D74
L75
L76
R77
R78
V79
D80
D96
N102
D111
W112
R113
R117
Q118
R132
R135
R142
R146
R166
Q169
R184
R189
Page 8 Full wwPDB NMR Structure Validation Report 2GF5
S190
G191
4.2.12 Score per residue for model 12
• Molecule 1: FADD protein
Chain A:
S1
S16
S17
L23
K24
R34
K35
L36
Q40
S41
G42
L43
D44
N53
E56
R64
R71
R72
H73
R77
R78
A91
F101
N102
D111
W112
R113
R114
L115
S122
R135
T138
E139
R140
S144
R166
Q169
M170
R184
N188
R189
S190
G191
4.2.13 Score per residue for model 13
• Molecule 1: FADD protein
Chain A:
S1
L5
H9
S18
L26
R34
K35
L36
E37
R38
S41
G42
H59
R64
R71
R72
H73
D74
R77
R78
A88
F101
N102
C105
R113
R117
K120
I126
R132
R135
R142
R146
N150
K153
R166
Q169
M170
E179
R184
D185
L186
R189
S190
G191
4.2.14 Score per residue for model 14
• Molecule 1: FADD protein
Chain A:
S1
K24
R34
K35
L36
N53
E56
H59
R64
R71
R72
H73
D74
R77
R78
F101
N102
R114
R117
Q118
I126
T138
R142
R146
K153
H160
R166
M170
Q181
R184
D185
R189
S190
G191
4.2.15 Score per residue for model 15
• Molecule 1: FADD protein
Chain A:
S1
L5
H9
L23
C27
K33
L36
G42
L43
E56
H59
R64
R71
D74
R77
R78
L97
F101
C105
K110
R113
R114
L115
K120
D131
R132
R146
K153
E154
A164
L165
R166
M170
L186
Page 9 Full wwPDB NMR Structure Validation Report 2GF5
R189
S190
G191
4.2.16 Score per residue for model 16
• Molecule 1: FADD protein
Chain A:
S1
D2
L15
L28
G29
R30
R34
K35
L36
E37
R38
N53
E61
R64
R71
R77
R78
V79
D80
L97
F101
N102
C105
K110
R113
R117
Q118
L119
K120
I126
I129
R132
Y133
P134
R135
T138
R142
R146
A156
T157
L165
R166
M170
R184
N188
R189
S190
G191
4.2.17 Score per residue for model 17
• Molecule 1: FADD protein
Chain A:
S1
E22
R30
K33
R34
K35
L36
E37
R38
N53
E56
H59
R64
E65
R71
R72
H73
D74
L75
L76
R77
R78
A88
F101
N102
K110
D111
W112
R113
R117
Q118
L119
K120
V121
I129
R132
R135
T138
E139
R140
V141
R142
R146
N150
E154
R166
Q169
M170
N171
L172
L186
Q187
N188
R189
S190
G191
4.2.18 Score per residue for model 18
• Molecule 1: FADD protein
Chain A:
S1
D2
L15
Y25
L28
G29
R30
K33
R34
K35
L36
E37
R38
G42
L43
E61
L62
L63
R64
R71
R72
H73
D74
R77
R78
V79
D80
P92
F101
N102
K110
R113
R114
L115
A116
R117
K120
I129
E130
D131
R132
R135
N136
R140
R166
Q169
M170
L176
R184
R189
S190
G191
4.2.19 Score per residue for model 19
• Molecule 1: FADD protein
Chain A:
Page 10 Full wwPDB NMR Structure Validation Report 2GF5
S1
D2
L5
H9
L26
R30
L36
E37
R38
L43
L50
L55
E56
P57
R64
L70
R71
R72
H73
D74
R78
F82
A86
A91
F101
N102
K110
D111
W112
R113
R114
R117
K120
D123
R132
Y133
P134
R135
T138
E139
R140
V141
R142
R146
E154
Q169
M170
A174
Q181
R184
R189
S190
G191
4.2.20 Score per residue for model 20
• Molecule 1: FADD protein
Chain A:
S1
S16
R30
R34
K35
L36
E37
R38
D44
N53
D54
L55
R64
R71
R78
V79
D80
A87
N102
D111
W112
R113
R114
R117
Q118
L119
K120
D127
R135
V141
R142
R146
E152
K153
E154
T157
R166
Q169
M170
L186
Q187
N188
G191
4.2.21 Score per residue for model 21
• Molecule 1: FADD protein
Chain A:
S1
L5
H9
L15
E22
R30
K33
R34
K35
L36
E37
R38
G42
L43
N53
E61
R64
L70
R71
R72
H73
D74
L75
L76
R77
R78
A87
F101
N102
R113
R114
R117
K120
R132
R135
T138
E139
R140
R146
R166
M170
R184
N188
R189
S190
G191
4.2.22 Score per residue for model 22 (medoid)
• Molecule 1: FADD protein
Chain A:
S1
S16
R30
R34
R38
G42
Q52
N53
D54
H59
T60
E61
R64
R71
D74
R77
E83
A90
F101
N102
D111
W112
R113
R114
R117
Q118
L119
K120
I129
R132
R135
T138
E139
R140
V141
R142
R146
Q169
R184
D185
L186
Q187
N188
R189
S190
G191
4.2.23 Score per residue for model 23
• Molecule 1: FADD protein
Page 11 Full wwPDB NMR Structure Validation Report 2GF5
Chain A:
S1
L5
H9
L15
R30
K33
L36
E37
R38
L43
N53
E56
L62
R71
R72
H73
D74
R77
D80
G85
L97
F101
N102
K110
R113
R114
R117
I129
R132
Y133
P134
R135
R140
R146
K153
H160
R166
Q169
M170
R184
R189
S190
G191
4.2.24 Score per residue for model 24
• Molecule 1: FADD protein
Chain A:
S1
D2
E19
R30
K33
R34
R38
V39
Q40
L43
Q52
E56
H59
R71
R72
H73
D74
R77
E95
F101
N102
R113
R114
R117
Q118
D127
R132
Y133
P134
R135
R140
V141
R142
R146
N150
T151
E152
K153
H160
R166
Q169
M170
R184
N188
R189
S190
G191
4.2.25 Score per residue for model 25
• Molecule 1: FADD protein
Chain A:
S1
L5
H9
L15
E19
E22
C27
R30
R34
K35
L36
E37
R38
G42
L43
E51
Q52
N53
H59
R64
R71
R72
H73
D74
R77
E83
N102
K110
R113
R114
R117
Q118
R135
T138
R146
R166
Q169
M170
R189
S190
G191
Page 12 Full wwPDB NMR Structure Validation Report 2GF5
5 Re�nement protocol and experimental data overview iO
The models were re�ned using the following method: simulated annealing.
Of the 100 calculated structures, 25 were deposited, based on the following criterion: 25 structures
for lowest energy.
The following table shows the software used for structure solution, optimisation and re�nement.
Software name Classi�cation VersionX-PLOR re�nement 2.12.2X-PLOR structure solution 2.12.2
No chemical shift data was provided. No validations of the models with respect to experimentalNMR restraints is performed at this time.
COVALENT-GEOMETRY INFOmissingINFO
5.1 Too-close contacts iO
In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in each chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashesaveraged over the ensemble.
Mol Chain Non-H H(model) H(added) Clashes1 A 1498 1517 1513 2±1All All 37450 37925 37825 38
The all-atom clashscore is de�ned as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 1.
All unique clashes are listed below, sorted by their clash magnitude.
Atom-1 Atom-2 Clash(Å) Distance(Å)Models
Worst Total
1:A:5:LEU:O 1:A:9:HIS:CD2 0.52 2.63 11 101:A:9:HIS:CD2 1:A:43:LEU:HD11 0.51 2.41 23 3
1:A:165:LEU:HD11 1:A:173:VAL:HG23 0.49 1.84 2 11:A:59:HIS:CE1 1:A:83:GLU:OE1 0.49 2.65 22 11:A:112:TRP:CD1 1:A:141:VAL:HG12 0.49 2.42 20 11:A:59:HIS:CD2 1:A:154:GLU:HG2 0.48 2.44 15 11:A:56:GLU:OE2 1:A:59:HIS:CD2 0.47 2.67 24 21:A:73:HIS:CE1 1:A:74:ASP:OD2 0.47 2.68 23 21:A:97:LEU:HD21 1:A:156:ALA:HB3 0.47 1.84 16 11:A:152:GLU:OE2 1:A:160:HIS:CE1 0.46 2.69 24 2
Continued on next page...
Page 13 Full wwPDB NMR Structure Validation Report 2GF5
Continued from previous page...
Atom-1 Atom-2 Clash(Å) Distance(Å)Models
Worst Total
1:A:119:LEU:HD21 1:A:164:ALA:HB2 0.46 1.87 3 11:A:55:LEU:H 1:A:55:LEU:CD2 0.45 2.24 20 11:A:82:PHE:HA 1:A:86:ALA:HB3 0.45 1.88 19 11:A:59:HIS:CD2 1:A:154:GLU:OE2 0.44 2.71 17 11:A:118:GLN:O 1:A:160:HIS:CE1 0.43 2.71 14 1
1:A:115:LEU:HD11 1:A:164:ALA:HA 0.43 1.91 15 11:A:111:ASP:HA 1:A:113:ARG:HH11 0.43 1.74 8 11:A:75:LEU:O 1:A:79:VAL:HG23 0.43 2.13 11 11:A:59:HIS:CE1 1:A:83:GLU:HB3 0.43 2.49 25 11:A:52:GLN:HA 1:A:52:GLN:HE21 0.42 1.73 5 11:A:152:GLU:OE1 1:A:160:HIS:CD2 0.42 2.71 7 11:A:73:HIS:CE1 1:A:74:ASP:OD1 0.42 2.73 18 11:A:133:TYR:CG 1:A:139:GLU:HG3 0.41 2.50 19 11:A:157:THR:OG1 1:A:160:HIS:CD2 0.41 2.74 4 1
5.2 Torsion angles iO
5.2.1 Protein backbone iO
In the following table, the Percentiles column shows the percent Ramachandran outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all NMRentries. The Analysed column shows the number of residues for which the backbone conformationwas analysed and the total number of residues.
Mol Chain Analysed Favoured Allowed Outliers Percentiles
1 A 189/191 (99%) 165±3 (87±2%) 21±3 (11±2%) 3±1 (2±1%) 13 56
All All 4725/4775 (99%) 4128 (87%) 518 (11%) 79 (2%) 13 56
All 27 unique Ramachandran outliers are listed below. They are sorted by the frequency ofoccurrence in the ensemble.
Mol Chain Res Type Models (Total)1 A 169 GLN 121 A 42 GLY 101 A 53 ASN 81 A 120 LYS 61 A 87 ALA 51 A 110 LYS 51 A 27 CYS 31 A 16 SER 3
Continued on next page...
Page 14 Full wwPDB NMR Structure Validation Report 2GF5
Continued from previous page...
Mol Chain Res Type Models (Total)1 A 33 LYS 31 A 71 ARG 31 A 153 LYS 21 A 28 LEU 21 A 72 ARG 21 A 126 ILE 21 A 154 GLU 11 A 58 GLY 11 A 43 LEU 11 A 134 PRO 11 A 123 ASP 11 A 121 VAL 11 A 44 ASP 11 A 112 TRP 11 A 122 SER 11 A 172 LEU 11 A 73 HIS 11 A 68 ALA 11 A 90 ALA 1
5.2.2 Protein sidechains iO
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 NMRentries. The Analysed column shows the number of residues for which the sidechain conformationwas analysed and the total number of residues.
Mol Chain Analysed Rotameric Outliers Percentiles
1 A 165/166 (99%) 149±3 (90±2%) 16±3 (10±2%) 12 58
All All 4125/4150 (99%) 3730 (90%) 395 (10%) 12 58
All 92 unique residues with a non-rotameric sidechain are listed below. They are sorted by thefrequency of occurrence in the ensemble.
Mol Chain Res Type Models (Total)1 A 102 ASN 231 A 36 LEU 221 A 71 ARG 151 A 74 ASP 121 A 138 THR 121 A 77 ARG 10
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Mol Chain Res Type Models (Total)1 A 56 GLU 101 A 188 ASN 101 A 101 PHE 101 A 170 MET 91 A 129 ILE 91 A 118 GLN 91 A 53 ASN 81 A 33 LYS 81 A 120 LYS 81 A 186 LEU 81 A 30 ARG 71 A 114 ARG 71 A 169 GLN 71 A 2 ASP 71 A 150 ASN 61 A 97 LEU 61 A 153 LYS 61 A 15 LEU 61 A 43 LEU 51 A 184 ARG 51 A 113 ARG 51 A 105 CYS 51 A 61 GLU 51 A 126 ILE 51 A 73 HIS 51 A 154 GLU 41 A 35 LYS 41 A 80 ASP 41 A 34 ARG 41 A 52 GLN 31 A 59 HIS 31 A 172 LEU 31 A 19 GLU 31 A 55 LEU 31 A 189 ARG 31 A 24 LYS 31 A 23 LEU 31 A 165 LEU 31 A 110 LYS 31 A 140 ARG 31 A 62 LEU 31 A 27 CYS 3
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Mol Chain Res Type Models (Total)1 A 117 ARG 31 A 51 GLU 31 A 92 PRO 21 A 131 ASP 21 A 16 SER 21 A 132 ARG 21 A 111 ASP 21 A 18 SER 21 A 135 ARG 21 A 26 LEU 21 A 185 ASP 21 A 45 LEU 21 A 40 GLN 21 A 115 LEU 21 A 127 ASP 21 A 22 GLU 21 A 70 LEU 21 A 96 ASP 21 A 76 LEU 21 A 54 ASP 21 A 49 LEU 21 A 38 ARG 21 A 181 GLN 21 A 119 LEU 21 A 65 GLU 11 A 125 LYS 11 A 11 VAL 11 A 136 ASN 11 A 44 ASP 11 A 190 SER 11 A 95 GLU 11 A 64 ARG 11 A 139 GLU 11 A 142 ARG 11 A 50 LEU 11 A 182 GLN 11 A 179 GLU 11 A 69 SER 11 A 176 LEU 11 A 81 ASP 11 A 123 ASP 11 A 187 GLN 1
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Mol Chain Res Type Models (Total)1 A 166 ARG 11 A 173 VAL 1
5.2.3 RNA iO
There are no RNA molecules in this entry.
5.3 Non-standard residues in protein, DNA, RNA chains iO
There are no non-standard protein/DNA/RNA residues in this entry.
5.4 Carbohydrates iO
There are no carbohydrates in this entry.
5.5 Ligand geometry iO
There are no ligands in this entry.
5.6 Other polymers iO
There are no such molecules in this entry.
5.7 Polymer linkage issues iO
There are no chain breaks in this entry.
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6 Chemical shift validation iO
No chemical shift data were provided