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Full wwPDB NMR Structure Validation Report i○
Feb 18, 2018 – 11:14 pm GMT
PDB ID : 2M8TTitle : Solution NMR structure of the V209M variant of the human prion protein
(residues 90-231)Authors : Mills, J.L.; Surewicz, K.; Surewicz, W.; Soennichsen, F.D.
Deposited on : 2013-05-28
This is a Full wwPDB NMR Structure 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/NMRValidationReportHelpwith 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:
Cyrange : Kirchner and Güntert (2011)NmrClust : Kelley et al. (1996)
MolProbity : 4.02b-467Percentile statistics : 20171227.v01 (using entries in the PDB archive December 27th 2017)
RCI : v_1n_11_5_13_A (Berjanski et al., 2005)PANAV : Wang et al. (2010)
ShiftChecker : trunk30686Ideal geometry (proteins) : Engh & Huber (2001)
Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : trunk30686
Page 2 Full wwPDB NMR Structure Validation Report 2M8T
1 Overall quality at a glance i○
The following experimental techniques were used to determine the structure:SOLUTION NMR
The overall completeness of chemical shifts assignment is 76%.
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)
NMR archive(#Entries)
Clashscore 136279 12091Ramachandran outliers 132675 10835
Sidechain outliers 132484 10811
The table below summarises the geometric issues observed across the polymeric chains and theirfit 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-defined 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 146
Page 3 Full wwPDB NMR Structure Validation Report 2M8T
2 Ensemble composition and analysis i○
This entry contains 20 models. Model 17 is the overall representative, medoid model (most similarto other models). The authors have identified model 1 as representative, based on the followingcriterion: fewest violations.
The following residues are included in the computation of the global validation metrics.
Well-defined (core) protein residuesWell-defined core Residue range (total) Backbone RMSD (Å) Medoid model
1 A:128-A:164, A:172-A:225(91)
0.56 17
Ill-defined 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 2 clusters and 3 single-model clusters were found.
Cluster number Models1 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 192 13, 20
Single-model clusters 3; 14; 18
Page 4 Full wwPDB NMR Structure Validation Report 2M8T
3 Entry composition i○
There is only 1 type of molecule in this entry. The entry contains 1777 atoms, of which 856 arehydrogens and 0 are deuteriums.
• Molecule 1 is a protein called Major prion protein.
Mol Chain Residues Atoms Trace
1 A 112 Total C H N O S1777 569 856 161 181 10 0
There are 5 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceA 86 GLY - EXPRESSION TAG UNP P04156A 87 SER - EXPRESSION TAG UNP P04156A 88 ASP - EXPRESSION TAG UNP P04156A 89 PRO - EXPRESSION TAG UNP P04156A 209 MET VAL ENGINEERED MUTATION UNP P04156
Page 5 Full wwPDB NMR Structure Validation Report 2M8T
4 Residue-property plots i○
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 first 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 classified as ill-defined 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 final structure are shown in grey.
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
F141
E146
R151
Y157
Q160
P165
M166
D167
E168
Y169
S170
N171
Q186
M206
E207
R208
M209
Y226
Q227
R228
G229
S230
S231
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: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
L130
D147
R151
Q160
Y163
R164
P165
M166
D167
E168
Y169
S170
N171
C179
R208
R220
Q223
Y226
Q227
R228
G229
S230
S231
4.2.2 Score per residue for model 2
• Molecule 1: Major prion protein
Chain A:
Page 6 Full wwPDB NMR Structure Validation Report 2M8T
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
Y128
M129
L130
G131
S132
A133
M134
P137
F141
E146
D147
R148
Q160
V161
P165
M166
D167
E168
Y169
S170
N171
H177
V180
Q186
M206
V210
M213
T216
R220
Q223
Y226
Q227
R228
G229
S230
S231
4.2.3 Score per residue for model 3
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
Y128
F141
E146
D147
R148
R151
M154
Q160
P165
M166
D167
E168
Y169
S170
N171
Q186
M206
E207
R208
M209
A224
Y225
Y226
Q227
R228
G229
S230
S231
4.2.4 Score per residue for model 4
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
Y128
M129
M134
I139
H140
F141
E146
R156
Y157
P158
N159
Q160
P165
M166
D167
E168
Y169
S170
N171
H177
I184
K185
Q186
T192
E196
K204
E207
R208
M209
Q212
M213
R220
Q223
Y226
Q227
R228
G229
S230
S231
4.2.5 Score per residue for model 5
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
G131
S132
A133
S143
Y149
Y157
P158
N159
Q160
V161
P165
M166
D167
E168
Y169
S170
N171
V176
N181
I182
Q186
M205
R208
M209
V210
E211
Q212
M213
C214
Y226
Q227
R228
G229
S230
S231
4.2.6 Score per residue for model 6
• Molecule 1: Major prion protein
Page 7 Full wwPDB NMR Structure Validation Report 2M8T
Chain A:GL
YSE
RAS
PPR
OGL
YGL
NGL
YGL
YGL
YTH
RHI
SSE
RGL
NTR
PAS
NLY
SPR
OSE
RLY
SPR
OLY
STH
RAS
NME
TLY
SHI
SME
TAL
AGL
YAL
AAL
AAL
AAL
AGL
YA1
20V1
21V1
22G1
23G1
24L1
25G1
26G1
27
I139
H140
F141
E146
R151
M154
P158
V161
P165
M166
D167
E168
Y169
S170
N171
F175
N181
I184
T191
M206
E207
R208
M209
M213
Y226
Q227
R228
G229
S230
S231
4.2.7 Score per residue for model 7
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
L130
A133
F141
G142
S143
E146
M154
Y157
P158
N159
Q160
P165
M166
D167
E168
Y169
S170
N171
V203
M206
E207
R208
M209
Y226
Q227
R228
G229
S230
S231
4.2.8 Score per residue for model 8
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
Y128
M129
L130
G131
S132
A133
F141
E146
R151
M154
N159
Q160
V161
P165
M166
D167
E168
Y169
S170
N171
R208
M209
V210
Y226
Q227
R228
G229
S230
S231
4.2.9 Score per residue for model 9
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
Y128
M129
L130
R136
I139
H140
F141
E146
D147
R151
M154
Y157
P158
N159
Q160
V161
Y162
P165
M166
D167
E168
Y169
S170
N171
N181
I184
K185
Q186
M206
E207
R208
M209
Q217
Y218
E219
R220
E221
Y225
Y226
Q227
R228
G229
S230
S231
Page 8 Full wwPDB NMR Structure Validation Report 2M8T
4.2.10 Score per residue for model 10
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
L130
G131
I138
F141
E146
D147
Y150
R151
Y157
P158
N159
Q160
P165
M166
D167
E168
Y169
S170
N171
D178
I182
Q186
E196
N197
M206
M209
Y226
Q227
R228
G229
S230
S231
4.2.11 Score per residue for model 11
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
Y128
R136
S143
D144
Y145
Y149
M154
Y157
V161
P165
M166
D167
E168
Y169
S170
N171
V180
I184
K185
Q186
E196
D202
V203
M206
E207
R208
M209
V210
M213
T216
R220
Y226
Q227
R228
G229
S230
S231
4.2.12 Score per residue for model 12
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
Y128
I139
H140
F141
D144
Y145
E146
D147
R148
R151
M154
Y157
V161
Y162
Y163
R164
P165
M166
D167
E168
Y169
S170
N171
Q172
F175
V176
C179
I184
M206
E207
R208
M209
V210
M213
C214
I215
T216
R220
Y226
Q227
R228
G229
S230
S231
4.2.13 Score per residue for model 13
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
L130
A133
F141
E146
D147
R151
Q160
P165
M166
D167
E168
Y169
S170
N171
Q172
Q186
M206
M209
M213
Q217
E221
Y226
Q227
R228
G229
S230
S231
Page 9 Full wwPDB NMR Structure Validation Report 2M8T
4.2.14 Score per residue for model 14
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
Y128
M129
I139
H140
F141
D147
R151
Q160
P165
M166
D167
E168
Y169
S170
N171
I184
K185
Q186
T191
V203
M206
E207
R208
M209
Q212
E219
Y226
Q227
R228
G229
S230
S231
4.2.15 Score per residue for model 15
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
L130
I139
H140
F141
E146
Y157
P158
N159
Q160
V161
P165
M166
D167
E168
Y169
S170
N171
H177
V180
I184
M206
E207
R208
M209
V210
Y226
Q227
R228
G229
S230
S231
4.2.16 Score per residue for model 16
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
Y128
F141
E146
R151
E152
N153
M154
H155
R156
Y157
P158
N159
Q160
V161
P165
M166
D167
E168
Y169
S170
N171
Q172
Q186
T201
R208
M209
V210
M213
T216
R220
Q223
Y226
Q227
R228
G229
S230
S231
4.2.17 Score per residue for model 17 (medoid)
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
Y128
A133
F141
G142
S143
E146
Q160
V161
P165
M166
D167
E168
Y169
S170
N171
Q172
F175
I184
K185
E196
M206
E207
R208
M209
V210
M213
Y226
Q227
R228
G229
S230
S231
Page 10 Full wwPDB NMR Structure Validation Report 2M8T
4.2.18 Score per residue for model 18
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
Y128
M129
L130
N153
Y157
Q160
V161
Y162
P165
M166
D167
E168
Y169
S170
N171
C179
I184
T201
M206
E207
R208
M209
M213
C214
Q217
R220
Q223
Y226
Q227
R228
G229
S230
S231
4.2.19 Score per residue for model 19
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
A133
F141
G142
S143
E146
R151
M154
N159
P165
M166
D167
E168
Y169
S170
N171
V180
Q186
G195
E196
N197
F198
T199
V203
K204
M205
M206
E207
R208
M209
V210
Y226
Q227
R228
G229
S230
S231
4.2.20 Score per residue for model 20
• Molecule 1: Major prion protein
Chain A:
GLY
SER
ASP
PRO
GLY
GLN
GLY
GLY
GLY
THR
HIS
SER
GLN
TRP
ASN
LYS
PRO
SER
LYS
PRO
LYS
THR
ASN
MET
LYS
HIS
MET
ALA
GLY
ALA
ALA
ALA
ALA
GLY
A120
V121
V122
G123
G124
L125
G126
G127
A133
H140
Y157
P158
N159
Q160
P165
M166
D167
E168
Y169
S170
N171
Q172
N173
N174
H177
V180
Q186
T191
E196
E200
K204
R208
Y226
Q227
R228
G229
S230
S231
Page 11 Full wwPDB NMR Structure Validation Report 2M8T
5 Refinement protocol and experimental data overview i○
The models were refined using the following method: simulated annealing, molecular dynamics,MOLECULAR DYNAMICS.
Of the 100 calculated structures, 20 were deposited, based on the following criterion: structureswith the least restraint violations.
The following table shows the software used for structure solution, optimisation and refinement.
Software name Classification VersionTALOS geometry optimizationCYANA structure solutionCNS geometry optimizationCYANA refinementCNS refinement
The following table shows chemical shift validation statistics as aggregates over all chemical shiftfiles. Detailed validation can be found in section 7 of this report.
Chemical shift file(s) 2m8t_cs.strNumber of chemical shift lists 1Total number of shifts 1503Number of shifts mapped to atoms 1503Number of unparsed shifts 0Number of shifts with mapping errors 0Number of shifts with mapping warnings 0Assignment completeness (well-defined parts) 76%
No validations of the models with respect to experimental NMR restraints is performed at thistime.
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6 Model quality i○
6.1 Standard geometry i○
There are no covalent bond-length or bond-angle outliers.
There are no bond-length outliers.
There are no bond-angle outliers.
There are no chirality outliers.
There are no planarity outliers.
6.2 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 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 772 721 723 9±3All All 15440 14420 14460 171
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 6.
All unique clashes are listed below, sorted by their clash magnitude.
Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:191:THR:HB 1:A:196:GLU:HB3 0.78 1.53 20 11:A:204:LYS:HE2 1:A:204:LYS:HA 0.76 1.57 4 11:A:130:LEU:HD11 1:A:160:GLN:HG3 0.67 1.65 13 91:A:153:ASN:O 1:A:156:ARG:HG2 0.63 1.93 16 1
1:A:163:TYR:HB3 1:A:179:CYS:HB3 0.62 1.71 12 11:A:161:VAL:HG13 1:A:213:MET:SD 0.60 2.37 16 41:A:220:ARG:HA 1:A:223:GLN:HG2 0.59 1.74 2 41:A:154:MET:HA 1:A:157:TYR:CD2 0.58 2.34 11 21:A:180:VAL:HA 1:A:210:VAL:HG11 0.58 1.74 11 41:A:147:ASP:O 1:A:151:ARG:HG2 0.57 1.98 13 2
1:A:139:ILE:HD12 1:A:208:ARG:HG3 0.56 1.77 15 51:A:156:ARG:HE 1:A:156:ARG:HA 0.56 1.60 4 11:A:133:ALA:HB2 1:A:160:GLN:HB3 0.56 1.77 5 51:A:206:MET:O 1:A:210:VAL:HG23 0.55 2.02 15 5
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:195:GLY:O 1:A:196:GLU:HG2 0.54 2.03 19 11:A:143:SER:HB2 1:A:146:GLU:OE2 0.53 2.03 7 21:A:206:MET:HA 1:A:209:MET:HG2 0.53 1.81 15 131:A:157:TYR:HB3 1:A:158:PRO:HD2 0.53 1.79 9 81:A:192:THR:HA 1:A:196:GLU:O 0.52 2.05 4 11:A:203:VAL:O 1:A:206:MET:HG2 0.52 2.05 11 1
1:A:163:TYR:HB3 1:A:179:CYS:SG 0.51 2.45 1 11:A:161:VAL:HG11 1:A:210:VAL:HG13 0.51 1.82 17 61:A:145:TYR:O 1:A:149:TYR:HB2 0.51 2.05 11 11:A:134:MET:SD 1:A:137:PRO:HA 0.51 2.46 2 11:A:141:PHE:HB2 1:A:146:GLU:OE1 0.50 2.06 8 131:A:213:MET:O 1:A:217:GLN:HG2 0.50 2.07 13 11:A:151:ARG:O 1:A:154:MET:HG2 0.49 2.07 12 7
1:A:133:ALA:HB1 1:A:159:ASN:OD1 0.48 2.08 19 11:A:141:PHE:CD1 1:A:146:GLU:HG2 0.48 2.42 7 21:A:184:ILE:HD11 1:A:207:GLU:CA 0.48 2.39 6 31:A:147:ASP:O 1:A:151:ARG:HB2 0.48 2.09 9 2
1:A:200:GLU:HB3 1:A:204:LYS:NZ 0.47 2.24 20 11:A:147:ASP:HB3 1:A:151:ARG:NH2 0.47 2.23 10 11:A:184:ILE:CD1 1:A:206:MET:HG3 0.47 2.39 14 51:A:172:GLN:HG3 1:A:175:PHE:H 0.47 1.69 17 21:A:216:THR:O 1:A:220:ARG:HG3 0.47 2.09 2 41:A:209:MET:O 1:A:213:MET:HG3 0.47 2.09 4 31:A:178:ASP:O 1:A:182:ILE:HG12 0.47 2.09 10 1
1:A:149:TYR:CD2 1:A:205:MET:HG3 0.47 2.45 5 11:A:177:HIS:O 1:A:180:VAL:HB 0.47 2.10 20 1
1:A:153:ASN:HB3 1:A:157:TYR:CZ 0.46 2.44 18 11:A:134:MET:HB2 1:A:213:MET:SD 0.46 2.50 2 11:A:141:PHE:CD2 1:A:146:GLU:HG2 0.46 2.44 2 21:A:156:ARG:NE 1:A:156:ARG:HA 0.46 2.26 4 11:A:139:ILE:HD11 1:A:209:MET:HA 0.46 1.88 12 11:A:133:ALA:CB 1:A:160:GLN:HB3 0.46 2.40 7 11:A:181:ASN:O 1:A:185:LYS:HG2 0.45 2.12 9 1
1:A:184:ILE:HD11 1:A:207:GLU:HA 0.45 1.88 6 71:A:176:VAL:HA 1:A:214:CYS:SG 0.45 2.52 5 21:A:141:PHE:CZ 1:A:208:ARG:HG3 0.45 2.47 3 11:A:136:ARG:O 1:A:136:ARG:HG2 0.44 2.12 11 1
1:A:149:TYR:HD2 1:A:205:MET:HG3 0.44 1.71 5 11:A:202:ASP:O 1:A:206:MET:HE2 0.44 2.12 11 1
1:A:144:ASP:OD2 1:A:148:ARG:HD3 0.44 2.12 12 11:A:139:ILE:HG21 1:A:141:PHE:CE2 0.44 2.48 14 1
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:217:GLN:O 1:A:221:GLU:HG2 0.43 2.13 9 11:A:204:LYS:CE 1:A:204:LYS:HA 0.43 2.38 4 11:A:134:MET:HE3 1:A:213:MET:HG2 0.43 1.90 4 11:A:182:ILE:O 1:A:186:GLN:HG2 0.43 2.14 5 1
1:A:185:LYS:HB2 1:A:185:LYS:NZ 0.42 2.29 17 11:A:157:TYR:CE2 1:A:206:MET:HB3 0.42 2.50 12 11:A:185:LYS:HB2 1:A:185:LYS:HZ2 0.41 1.75 17 11:A:199:THR:O 1:A:203:VAL:HG23 0.41 2.16 19 11:A:209:MET:SD 1:A:210:VAL:HG13 0.41 2.56 16 11:A:129:MET:HA 1:A:129:MET:CE 0.41 2.46 4 11:A:138:ILE:HA 1:A:150:TYR:CE2 0.41 2.51 10 11:A:179:CYS:HB2 1:A:214:CYS:SG 0.41 2.56 18 11:A:203:VAL:O 1:A:207:GLU:HB2 0.41 2.16 7 11:A:203:VAL:O 1:A:207:GLU:HG3 0.40 2.16 14 11:A:162:TYR:N 1:A:162:TYR:CD1 0.40 2.89 9 11:A:133:ALA:HA 1:A:160:GLN:HB3 0.40 1.94 20 11:A:184:ILE:HG13 1:A:207:GLU:HG2 0.40 1.93 15 11:A:146:GLU:CD 1:A:146:GLU:H 0.40 2.19 15 11:A:157:TYR:HD2 1:A:209:MET:SD 0.40 2.40 12 11:A:209:MET:HG3 1:A:210:VAL:N 0.40 2.31 12 1
6.3 Torsion angles i○
6.3.1 Protein backbone i○
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 91/146 (62%) 87±1 (95±2%) 4±1 (4±1%) 0±1 (0±1%) 40 79
All All 1820/2920 (62%) 1736 (95%) 76 (4%) 8 (0%) 40 79
All 4 unique Ramachandran outliers are listed below. They are sorted by the frequency of occur-rence in the ensemble.
Mol Chain Res Type Models (Total)1 A 131 GLY 41 A 141 PHE 2
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Continued from previous page...Mol Chain Res Type Models (Total)1 A 142 GLY 11 A 196 GLU 1
6.3.2 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 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 86/123 (70%) 82±2 (96±2%) 4±2 (4±2%) 37 83
All All 1720/2460 (70%) 1648 (96%) 72 (4%) 37 83
All 26 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 208 ARG 111 A 186 GLN 111 A 160 GLN 71 A 129 MET 31 A 143 SER 31 A 212 GLN 31 A 196 GLU 31 A 177 HIS 31 A 151 ARG 31 A 159 ASN 21 A 172 GLN 21 A 201 THR 21 A 181 ASN 21 A 148 ARG 21 A 191 THR 21 A 136 ARG 21 A 219 GLU 21 A 221 GLU 11 A 158 PRO 11 A 162 TYR 11 A 197 ASN 11 A 156 ARG 11 A 204 LYS 1
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Continued from previous page...Mol Chain Res Type Models (Total)1 A 198 PHE 11 A 217 GLN 11 A 140 HIS 1
6.3.3 RNA i○
There are no RNA molecules in this entry.
6.4 Non-standard residues in protein, DNA, RNA chains i○
There are no non-standard protein/DNA/RNA residues in this entry.
6.5 Carbohydrates i○
There are no carbohydrates in this entry.
6.6 Ligand geometry i○
There are no ligands in this entry.
6.7 Other polymers i○
There are no such molecules in this entry.
6.8 Polymer linkage issues i○
There are no chain breaks in this entry.
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7 Chemical shift validation i○
The completeness of assignment taking into account all chemical shift lists is 76% for the well-defined parts and 74% for the entire structure.
7.1 Chemical shift list 1
File name: 2m8t_cs.str
Chemical shift list name: assigned_chem_shift_list_1
7.1.1 Bookkeeping i○
The following table shows the results of parsing the chemical shift list and reports the number ofnuclei with statistically unusual chemical shifts.
Total number of shifts 1503Number of shifts mapped to atoms 1503Number of unparsed shifts 0Number of shifts with mapping errors 0Number of shifts with mapping warnings 0Number of shift outliers (ShiftChecker) 0
7.1.2 Chemical shift referencing i○
The following table shows the suggested chemical shift referencing corrections.
Nucleus # values Correction ± precision, ppm Suggested action13Cα 142 -0.26 ± 0.16 None needed (< 0.5 ppm)13Cβ 125 0.09 ± 0.10 None needed (< 0.5 ppm)13C′ 0 — None (insufficient data)15N 133 0.06 ± 0.19 None needed (< 0.5 ppm)
7.1.3 Completeness of resonance assignments i○
The following table shows the completeness of the chemical shift assignments for the well-definedregions of the structure. The overall completeness is 76%, i.e. 906 atoms were assigned a chemicalshift out of a possible 1187. 7 out of 7 assigned methyl groups (LEU and VAL) were assignedstereospecifically.
Total 1H 13C 15NBackbone 352/451 (78%) 173/180 (96%) 91/182 (50%) 88/89 (99%)Sidechain 482/609 (79%) 297/360 (82%) 166/213 (78%) 19/36 (53%)
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Continued from previous page...Total 1H 13C 15N
Aromatic 72/127 (57%) 51/67 (76%) 21/56 (38%) 0/4 (0%)Overall 906/1187 (76%) 521/607 (86%) 278/451 (62%) 107/129 (83%)
The following table shows the completeness of the chemical shift assignments for the full structure.The overall completeness is 74%, i.e. 1048 atoms were assigned a chemical shift out of a possible1407. 10 out of 10 assigned methyl groups (LEU and VAL) were assigned stereospecifically.
Total 1H 13C 15NBackbone 416/554 (75%) 205/221 (93%) 108/224 (48%) 103/109 (94%)Sidechain 548/710 (77%) 337/420 (80%) 189/249 (76%) 22/41 (54%)Aromatic 84/143 (59%) 59/75 (79%) 25/64 (39%) 0/4 (0%)Overall 1048/1407 (74%) 601/716 (84%) 322/537 (60%) 125/154 (81%)
7.1.4 Statistically unusual chemical shifts i○
There are no statistically unusual chemical shifts.
7.1.5 Random Coil Index (RCI) plots i○
The image below reports random coil index values for the protein chains in the structure. Theheight of each bar gives a probability of a given residue to be disordered, as predicted fromthe available chemical shifts and the amino acid sequence. A value above 0.2 is an indicationof significant predicted disorder. The colour of the bar shows whether the residue is in the well-defined core (black) or in the ill-defined residue ranges (cyan), as described in section 2 on ensemblecomposition.
Random coil index (RCI) for chain A:
