full wwpdb nmr structure validation report i · i149 f152 q153 i154 l155 e156 n157 q158 a159 4.2.4...
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Full wwPDB NMR Structure Validation Report i○
Feb 20, 2018 – 10:17 pm GMT
PDB ID : 2KKITitle : Solution structure of human Interleukin 1a
Authors : Mohan, S.K.; Chang, H.-K.; Yu, C.Deposited on : 2009-06-24
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 2KKI
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 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.
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 151
Page 3 Full wwPDB NMR Structure Validation Report 2KKI
2 Ensemble composition and analysis i○
This entry contains 14 models. Model 11 is the overall representative, medoid model (most similarto other models). The authors have identified model 1 as representative, based on the followingcriterion: lowest energy.
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:13-A:144, A:148-A:159(144)
0.36 11
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 3 clusters and 2 single-model clusters were found.
Cluster number Models1 6, 8, 9, 13, 142 5, 7, 11, 123 1, 2, 4
Single-model clusters 3; 10
Page 4 Full wwPDB NMR Structure Validation Report 2KKI
3 Entry composition i○
There is only 1 type of molecule in this entry. The entry contains 2423 atoms, of which 1208 arehydrogens and 0 are deuteriums.
• Molecule 1 is a protein called Interleukin-1 alpha.
Mol Chain Residues Atoms Trace
1 A 151 Total C H N O S2423 782 1208 197 232 4 0
Page 5 Full wwPDB NMR Structure Validation Report 2KKI
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: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
N13
F14
M15
R16
I17
I18
K19
Y20
E21
F22
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
R34
L40
T41
A42
L45
L48
D49
E50
A51
V52
K53
F54
D55
M56
G57
A58
Y59
K60
D64
K67
I68
T69
V70
I71
L72
R73
I74
L79
Y80
V81
T82
A83
Q84
D85
E86
D87
Q88
P89
V90
L91
L92
K93
E97
T101
I102
T103
G104
S105
E106
T107
N108
L109
L110
F111
F112
K119
N120
Y121
F122
T123
S124
V125
A126
H127
P128
N129
L130
F131
I132
A133
T134
K135
Q136
D137
Y138
W139
V140
C141
L142
A143
G144
G145
P146
P147
S148
I149
T150
D151
F152
Q153
I154
L155
E156
N157
Q158
A159
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: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
N13
F14
M15
R16
I17
I18
K19
Y20
E21
F22
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
R34
L40
T41
A42
L45
H46
N47
L48
D49
E50
A51
V52
K53
F54
D55
M56
G57
A58
Y59
K60
S61
D64
D65
A66
K67
V70
I71
L72
R73
I74
L79
Y80
V81
T82
A83
Q84
D85
E86
D87
Q88
P89
V90
L91
L92
K93
E94
I98
P99
K100
T101
I102
T103
G104
S105
E106
T107
N108
L109
L110
F111
F112
W113
E114
K119
F122
T123
S124
V125
A126
H127
P128
N129
L130
F131
I132
A133
T134
K135
Q136
W139
V140
C141
L142
A143
G144
G145
P146
P147
S148
I149
T150
D151
F152
Q153
I154
L155
E156
N157
Q158
A159
Page 6 Full wwPDB NMR Structure Validation Report 2KKI
4.2.2 Score per residue for model 2
• Molecule 1: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
N13
F14
M15
R16
I17
I18
K19
Y20
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
R34
D37
L40
T41
A42
L45
L48
D49
E50
A51
V52
K53
F54
D55
M56
Y59
D64
K67
I68
T69
V70
I71
L72
R73
L79
Y80
V81
T82
A83
E86
D87
Q88
P89
V90
L91
L92
K93
E97
K100
T101
I102
T103
G104
S105
E106
T107
N108
L109
L110
F111
F112
K119
N120
Y121
F122
T123
S124
V125
A126
H127
P128
N129
L130
F131
I132
A133
T134
K135
Q136
D137
Y138
W139
V140
C141
L142
A143
G144
G145
P146
P147
S148
I149
T150
D151
F152
L155
E156
N157
Q158
A159
4.2.3 Score per residue for model 3
• Molecule 1: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
N13
F14
M15
R16
I17
I18
K19
Y20
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
R34
L40
T41
A42
A43
A44
L45
H46
N47
L48
D49
E50
A51
V52
K53
F54
D55
M56
Y59
K60
D64
K67
I68
T69
V70
I71
L72
R73
I74
S75
K76
Y80
V81
T82
E86
D87
Q88
P89
V90
L91
L92
K93
E94
M95
P96
E97
I98
P99
K100
T101
I102
T103
G104
S105
E106
T107
N108
L109
L110
F111
F112
K119
N120
Y121
F122
T123
S124
H127
P128
N129
L130
F131
I132
A133
T134
K135
Q136
W139
V140
C141
L142
A143
G144
G145
P146
P147
S148
I149
F152
Q153
I154
L155
E156
N157
Q158
A159
4.2.4 Score per residue for model 4
• Molecule 1: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
I18
K19
Y20
E21
F22
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
R34
A35
L40
T41
A42
L45
L48
D49
E50
A51
V52
K53
F54
D55
M56
G57
A58
Y59
D64
K67
I68
T69
V70
I71
L72
R73
I74
S75
K76
L79
Y80
V81
T82
E86
D87
Q88
P89
V90
L91
L92
K93
I102
T103
G104
S105
E106
T107
N108
L109
L110
F111
F112
W113
E114
K119
N120
Y121
F122
T123
S124
V125
A126
H127
P128
N129
L130
F131
I132
A133
T134
K135
Q136
V140
C141
L142
A143
G144
G145
P146
P147
S148
I149
T150
D151
F152
L155
E156
N157
Q158
A159
Page 7 Full wwPDB NMR Structure Validation Report 2KKI
4.2.5 Score per residue for model 5
• Molecule 1: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
N13
F14
M15
R16
I17
I18
K19
F22
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
R34
L40
T41
A42
L45
L48
D49
E50
K53
F54
D55
M56
G57
A58
Y59
K60
D64
T69
V70
I71
L72
R73
I74
S75
K76
T77
Q78
L79
Y80
V81
T82
A83
E86
D87
Q88
P89
V90
L91
L92
K93
E97
K100
T101
I102
T103
G104
S105
E106
T107
N108
L109
L110
F111
T115
K119
N120
Y121
F122
T123
S124
H127
L130
F131
I132
A133
T134
K135
Q136
D137
Y138
W139
V140
C141
L142
G145
P146
P147
S148
I149
T150
D151
F152
Q153
I154
L155
E156
A159
4.2.6 Score per residue for model 6
• Molecule 1: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
N13
F14
M15
R16
I17
I18
K19
Y20
E21
F22
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
R34
L40
T41
A42
L45
L48
D49
E50
A51
F54
D55
M56
Y59
K60
D64
K67
I68
T69
V70
I71
L72
R73
I74
L79
Y80
V81
T82
A83
Q84
D85
E86
D87
Q88
P89
V90
L91
L92
K93
I98
P99
K100
T101
I102
T103
G104
S105
E106
T107
N108
L109
L110
F111
F112
K119
N120
Y121
F122
T123
S124
V125
A126
H127
P128
N129
L130
F131
I132
A133
T134
K135
Q136
D137
Y138
W139
V140
C141
L142
A143
G144
G145
P146
P147
S148
I149
T150
D151
F152
Q153
I154
L155
E156
N157
Q158
A159
4.2.7 Score per residue for model 7
• Molecule 1: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
N13
F14
M15
R16
I17
I18
K19
F22
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
R34
A35
L40
T41
A42
A43
A44
L45
L48
D49
E50
A51
V52
K53
F54
D55
M56
G57
A58
Y59
K60
D64
V70
I71
L72
R73
L79
Y80
V81
T82
A83
Q84
D85
E86
D87
Q88
P89
V90
L91
L92
K93
I98
P99
K100
T101
I102
T103
G104
N108
L109
L110
F111
F112
H116
K119
F122
T123
S124
H127
P128
N129
L130
F131
I132
A133
T134
K135
Q136
D137
Y138
C141
L142
A143
G144
G145
P146
P147
S148
I149
T150
D151
F152
Q153
I154
L155
E156
N157
Q158
A159
Page 8 Full wwPDB NMR Structure Validation Report 2KKI
4.2.8 Score per residue for model 8
• Molecule 1: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
N13
F14
M15
R16
I17
I18
K19
Y20
E21
F22
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
R34
L40
T41
A42
L45
H46
N47
L48
D49
E50
A51
V52
K53
F54
D55
M56
G57
A58
Y59
K60
D64
T69
V70
I71
L72
R73
I74
S75
K76
T77
Q78
L79
Y80
V81
T82
A83
Q84
D85
E86
D87
Q88
P89
V90
L91
L92
K93
E94
M95
P96
T101
I102
T103
G104
S105
E106
T107
N108
L109
L110
F111
K119
N120
Y121
F122
T123
S124
H127
L130
F131
I132
A133
T134
K135
Q136
D137
Y138
W139
V140
C141
L142
A143
G144
G145
P146
P147
S148
I149
T150
D151
F152
Q153
I154
L155
A159
4.2.9 Score per residue for model 9
• Molecule 1: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
N13
F14
M15
R16
I17
I18
K19
F22
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
R34
L40
T41
A42
A43
A44
L45
L48
D49
E50
A51
V52
K53
F54
D55
M56
G57
A58
Y59
K60
D64
T69
V70
I71
L72
R73
I74
T77
Y80
V81
T82
A83
Q84
D85
E86
D87
Q88
P89
V90
L91
L92
K93
E97
T101
I102
T103
G104
S105
E106
T107
N108
L109
L110
F111
K119
N120
Y121
F122
T123
S124
V125
N129
L130
F131
I132
A133
T134
K135
Y138
W139
V140
C141
L142
A143
G144
G145
P146
P147
S148
I149
T150
D151
F152
L155
E156
N157
Q158
A159
4.2.10 Score per residue for model 10
• Molecule 1: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
N13
F14
M15
R16
I17
I18
K19
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
L40
T41
A42
A43
A44
L45
L48
A51
V52
K53
F54
D55
M56
G57
A58
Y59
K60
D64
K67
I68
T69
V70
I71
L72
R73
Q78
L79
Y80
V81
T82
A83
Q84
D85
E86
D87
Q88
P89
V90
L91
L92
K93
P96
E97
I98
T101
I102
T103
G104
N108
L109
L110
F111
F112
K119
N120
Y121
F122
T123
S124
V125
A126
H127
P128
N129
L130
F131
I132
A133
T134
K135
Q136
D137
Y138
W139
V140
C141
L142
A143
G144
G145
P146
P147
S148
I149
T150
D151
F152
Q153
I154
L155
A159
Page 9 Full wwPDB NMR Structure Validation Report 2KKI
4.2.11 Score per residue for model 11 (medoid)
• Molecule 1: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
N13
F14
M15
R16
I17
I18
K19
Y20
E21
F22
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
R34
L40
T41
A42
A43
A44
L45
L48
D49
E50
K53
F54
D55
M56
G57
A58
Y59
K60
D64
K67
I68
T69
V70
I71
L72
R73
L79
Y80
V81
T82
A83
Q84
D85
E86
D87
Q88
P89
V90
L91
L92
K93
E94
M95
P96
E97
I98
T101
I102
T103
G104
S105
E106
T107
N108
L109
L110
F111
T115
K119
N120
Y121
F122
T123
S124
V125
A126
H127
P128
N129
L130
F131
I132
A133
T134
K135
Q136
V140
C141
L142
A143
G144
G145
P146
P147
S148
I149
T150
D151
F152
Q153
I154
L155
Q158
A159
4.2.12 Score per residue for model 12
• Molecule 1: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
N13
F14
M15
R16
I17
I18
K19
Y20
E21
F22
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
L40
T41
A42
A43
A44
L45
H46
N47
L48
D49
E50
A51
V52
K53
F54
D55
M56
G57
A58
Y59
K60
D64
K67
V70
I71
L72
R73
Q78
L79
Y80
V81
T82
A83
E86
D87
Q88
P89
V90
L91
L92
K93
E94
M95
P96
E97
T101
I102
T103
G104
S105
E106
T107
N108
L109
L110
F111
K119
N120
Y121
F122
T123
S124
V125
A126
H127
P128
N129
L130
F131
I132
A133
T134
K135
Q136
V140
C141
L142
A143
G144
G145
P146
P147
S148
I149
T150
D151
F152
Q153
I154
L155
E156
N157
Q158
A159
4.2.13 Score per residue for model 13
• Molecule 1: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
N13
F14
M15
R16
I17
I18
K19
Y20
E21
F22
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
R34
D37
L40
T41
A42
A43
A44
L45
H46
N47
L48
D49
E50
A51
V52
K53
F54
D55
M56
G57
A58
Y59
K60
D64
K67
V70
I71
L72
R73
I74
S75
K76
Y80
V81
T82
A83
E86
D87
Q88
P89
V90
L91
L92
K93
E97
I98
P99
K100
T101
I102
T103
G104
S105
E106
T107
N108
L109
L110
F111
E114
K119
N120
Y121
F122
T123
P128
N129
L130
F131
I132
A133
T134
K135
Q136
D137
Y138
W139
V140
C141
L142
A143
G144
G145
P146
P147
S148
I149
T150
D151
F152
Q153
I154
L155
E156
N157
Q158
A159
Page 10 Full wwPDB NMR Structure Validation Report 2KKI
4.2.14 Score per residue for model 14
• Molecule 1: Interleukin-1 alpha
Chain A:
N9 V10
K11
Y12
N13
F14
M15
R16
I17
I18
K19
Y20
E21
F22
I23
L24
N25
D26
A27
L28
N29
Q30
S31
I32
I33
L40
T41
A42
L45
H46
N47
L48
D49
E50
K53
F54
D55
M56
G57
A58
Y59
K60
D64
K67
I68
T69
V70
I71
L72
R73
L79
Y80
V81
T82
A83
E86
D87
Q88
P89
V90
L91
L92
K93
E94
M95
P96
E97
I98
T101
I102
T103
G104
S105
E106
T107
N108
L109
L110
F111
F112
W113
E114
T115
H116
K119
N120
Y121
F122
T123
S124
H127
L130
F131
I132
A133
T134
K135
Q136
V140
C141
L142
A143
G144
G145
P146
P147
S148
I149
T150
D151
F152
Q153
I154
L155
E156
N157
Q158
A159
Page 11 Full wwPDB NMR Structure Validation Report 2KKI
5 Refinement protocol and experimental data overview i○
The models were refined using the following method: simulated annealing.
Of the 200 calculated structures, 14 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 VersionCNS refinement
No chemical shift data was provided. No validations of the models with respect to experimentalNMR restraints is performed at this time.
Page 12 Full wwPDB NMR Structure Validation Report 2KKI
6 Model quality i○
6.1 Standard geometry i○
The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered an outlierworth inspection. RMSZ is the (average) root-mean-square of all Z scores of the bond lengths (orangles).
Mol Chain Bond lengths Bond anglesRMSZ #Z>5 RMSZ #Z>5
1 A 0.55±0.03 1±1/1185 (0.0±0.1%) 0.65±0.03 0±0/1607 (0.0±0.0%)All All 0.55 7/16590 (0.0%) 0.65 0/22498 (0.0%)
Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifyingif the center is modelled as a planar moiety or with the opposite hand. A planarity outlier isdetected by checking planarity of atoms in a peptide group, atoms in a mainchain group or atomsof a sidechain that are expected to be planar.
Mol Chain Chirality Planarity1 A 0.0±0.0 0.9±0.9All All 0 13
All unique bond outliers are listed below. They are sorted according to the Z-score of the worstoccurrence in the ensemble.
Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å) ModelsWorst Total
1 A 80 TYR CE1-CZ 8.31 1.49 1.38 11 21 A 59 TYR CE1-CZ 7.28 1.48 1.38 2 21 A 59 TYR CE2-CZ -6.55 1.30 1.38 2 11 A 131 PHE CE1-CZ 5.81 1.48 1.37 8 11 A 80 TYR CE2-CZ -5.39 1.31 1.38 11 1
There are no bond-angle outliers.
There are no chirality outliers.
All unique planar outliers are listed below. They are sorted by the frequency of occurrence in theensemble.
Mol Chain Res Type Group Models (Total)1 A 59 TYR Sidechain 51 A 80 TYR Sidechain 31 A 112 PHE Sidechain 2
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Page 13 Full wwPDB NMR Structure Validation Report 2KKI
Continued from previous page...Mol Chain Res Type Group Models (Total)1 A 131 PHE Sidechain 11 A 111 PHE Sidechain 11 A 121 TYR Sidechain 1
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 1161 1152 1149 106±9All All 16254 16128 16086 1490
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 46.
All unique clashes are listed below, sorted by their clash magnitude.
Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:20:TYR:CB 1:A:55:ASP:HA 1.01 1.86 14 11:A:20:TYR:HB3 1:A:55:ASP:HA 0.95 1.34 14 11:A:89:PRO:HA 1:A:141:CYS:HA 0.95 1.37 5 141:A:81:VAL:HB 1:A:111:PHE:HZ 0.93 1.24 3 91:A:31:SER:HB3 1:A:51:ALA:HB2 0.92 1.42 6 11:A:31:SER:HB2 1:A:51:ALA:HB2 0.92 1.42 1 51:A:49:ASP:HB2 1:A:157:ASN:HB2 0.91 1.40 6 61:A:131:PHE:CE1 1:A:150:THR:HG21 0.90 2.02 9 21:A:71:ILE:HG23 1:A:109:LEU:HD21 0.90 1.41 9 81:A:33:ILE:HG22 1:A:51:ALA:HA 0.89 1.44 9 11:A:123:THR:HA 1:A:131:PHE:HB2 0.89 1.43 9 11:A:23:ILE:HB 1:A:155:LEU:HB2 0.88 1.42 2 11
1:A:45:LEU:HD11 1:A:50:GLU:HB3 0.88 1.44 11 81:A:45:LEU:HD12 1:A:48:LEU:HA 0.87 1.46 1 11:A:86:GLU:HG3 1:A:87:ASP:H 0.86 1.30 3 61:A:30:GLN:HG3 1:A:136:GLN:HA 0.85 1.47 14 41:A:135:LYS:HE3 1:A:141:CYS:HB3 0.85 1.48 14 11:A:135:LYS:HD2 1:A:138:TYR:HB2 0.85 1.48 6 31:A:102:ILE:HG23 1:A:106:GLU:HB3 0.84 1.46 13 11:A:81:VAL:HB 1:A:111:PHE:CZ 0.83 2.08 3 9
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:102:ILE:HG23 1:A:106:GLU:HB2 0.83 1.48 1 41:A:33:ILE:HG12 1:A:51:ALA:HA 0.81 1.52 10 81:A:79:LEU:HD23 1:A:92:LEU:HD13 0.81 1.51 4 51:A:102:ILE:HG12 1:A:106:GLU:HB2 0.80 1.49 5 31:A:15:MET:HG3 1:A:16:ARG:HD2 0.80 1.51 8 11:A:112:PHE:CE2 1:A:125:VAL:HA 0.80 2.12 2 21:A:48:LEU:HB2 1:A:157:ASN:HA 0.80 1.53 7 31:A:24:LEU:HD21 1:A:152:PHE:HD1 0.79 1.38 4 11:A:130:LEU:HB3 1:A:142:LEU:HD21 0.79 1.52 9 31:A:119:LYS:HA 1:A:152:PHE:O 0.79 1.76 9 141:A:82:THR:HA 1:A:108:ASN:HB3 0.78 1.56 1 91:A:87:ASP:HA 1:A:142:LEU:O 0.78 1.78 8 141:A:28:LEU:HG 1:A:149:ILE:HG21 0.77 1.55 8 61:A:85:ASP:HA 1:A:130:LEU:HD22 0.77 1.57 6 2
1:A:82:THR:HG23 1:A:93:LYS:HG2 0.77 1.57 1 21:A:84:GLN:HG3 1:A:85:ASP:H 0.77 1.38 11 11:A:133:ALA:HB1 1:A:148:SER:HB3 0.76 1.55 9 121:A:133:ALA:CB 1:A:148:SER:HB3 0.76 2.10 4 91:A:86:GLU:O 1:A:142:LEU:HB3 0.76 1.80 9 141:A:31:SER:HB2 1:A:51:ALA:CB 0.76 2.11 12 61:A:45:LEU:HG 1:A:155:LEU:HD13 0.75 1.59 2 11:A:26:ASP:OD2 1:A:28:LEU:HB2 0.75 1.81 3 61:A:132:ILE:O 1:A:150:THR:HG23 0.75 1.82 4 11:A:56:MET:HA 1:A:71:ILE:O 0.74 1.83 12 141:A:131:PHE:HE1 1:A:150:THR:HG1 0.74 1.26 9 11:A:27:ALA:HB2 1:A:119:LYS:HD2 0.73 1.60 7 41:A:100:LYS:HD3 1:A:100:LYS:H 0.73 1.42 5 11:A:83:ALA:HB1 1:A:130:LEU:HD23 0.73 1.60 1 91:A:79:LEU:HD21 1:A:92:LEU:HD13 0.73 1.60 14 11:A:58:ALA:HA 1:A:70:VAL:HA 0.73 1.59 4 81:A:31:SER:HB2 1:A:45:LEU:HD23 0.72 1.61 4 71:A:131:PHE:HB3 1:A:143:ALA:O 0.72 1.82 8 71:A:26:ASP:OD2 1:A:134:THR:HB 0.72 1.84 8 51:A:59:TYR:HE2 1:A:110:LEU:HD22 0.72 1.42 2 11:A:23:ILE:HB 1:A:155:LEU:HD12 0.72 1.59 7 11:A:67:LYS:HE2 1:A:125:VAL:HA 0.72 1.60 6 31:A:28:LEU:HB3 1:A:136:GLN:HG2 0.72 1.58 10 31:A:19:LYS:HA 1:A:19:LYS:HE2 0.72 1.62 14 11:A:13:ASN:HB2 1:A:102:ILE:HG13 0.72 1.62 12 11:A:13:ASN:OD1 1:A:102:ILE:HB 0.72 1.83 11 31:A:81:VAL:HB 1:A:109:LEU:HD13 0.72 1.62 14 2
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:13:ASN:HB3 1:A:59:TYR:HB3 0.71 1.61 7 11:A:30:GLN:OE1 1:A:136:GLN:HA 0.71 1.84 12 11:A:57:GLY:H 1:A:71:ILE:HG13 0.71 1.46 13 4
1:A:26:ASP:OD1 1:A:28:LEU:HB2 0.71 1.85 4 41:A:24:LEU:O 1:A:31:SER:HA 0.70 1.86 4 131:A:133:ALA:O 1:A:140:VAL:HG23 0.70 1.86 4 31:A:129:ASN:HA 1:A:144:GLY:HA3 0.70 1.62 11 51:A:31:SER:CB 1:A:51:ALA:HB2 0.70 2.16 12 51:A:52:VAL:HB 1:A:74:ILE:HD13 0.70 1.63 13 11:A:80:TYR:CE2 1:A:109:LEU:HB2 0.70 2.22 5 11:A:40:LEU:HD13 1:A:92:LEU:HD11 0.69 1.62 7 51:A:45:LEU:HD11 1:A:50:GLU:CB 0.69 2.17 14 71:A:82:THR:HG23 1:A:93:LYS:HB3 0.69 1.63 4 31:A:82:THR:HG22 1:A:108:ASN:HB3 0.69 1.64 6 31:A:54:PHE:HA 1:A:73:ARG:O 0.69 1.87 3 131:A:35:ALA:HB2 1:A:41:THR:HG22 0.68 1.64 7 21:A:32:ILE:HB 1:A:40:LEU:HD21 0.68 1.65 3 5
1:A:15:MET:HG3 1:A:16:ARG:HG3 0.68 1.65 12 21:A:82:THR:CG2 1:A:93:LYS:HB3 0.68 2.18 4 21:A:134:THR:HA 1:A:140:VAL:HG12 0.68 1.65 9 21:A:18:ILE:HD12 1:A:56:MET:HG2 0.68 1.65 1 11:A:17:ILE:HD13 1:A:17:ILE:H 0.68 1.48 3 11:A:13:ASN:CB 1:A:59:TYR:HB2 0.68 2.19 8 21:A:23:ILE:HD13 1:A:53:LYS:HB3 0.67 1.64 2 51:A:24:LEU:HD21 1:A:152:PHE:CD1 0.67 2.22 4 11:A:28:LEU:HB2 1:A:30:GLN:HE22 0.67 1.50 11 11:A:86:GLU:HG2 1:A:87:ASP:H 0.67 1.49 13 81:A:13:ASN:ND2 1:A:59:TYR:HB2 0.67 2.04 6 21:A:27:ALA:H 1:A:151:ASP:HB2 0.67 1.50 10 7
1:A:21:GLU:HG3 1:A:53:LYS:HD2 0.67 1.66 11 21:A:86:GLU:HG3 1:A:87:ASP:N 0.67 2.05 11 61:A:120:ASN:HB3 1:A:152:PHE:CD1 0.67 2.24 2 41:A:26:ASP:HB3 1:A:134:THR:OG1 0.67 1.88 9 51:A:32:ILE:HA 1:A:42:ALA:HA 0.67 1.65 2 13
1:A:28:LEU:HD21 1:A:149:ILE:HG13 0.66 1.65 12 71:A:80:TYR:CD2 1:A:109:LEU:HD22 0.66 2.24 3 41:A:28:LEU:HD13 1:A:136:GLN:HB2 0.66 1.66 1 51:A:28:LEU:HD13 1:A:136:GLN:HG3 0.66 1.67 2 21:A:28:LEU:HD11 1:A:149:ILE:HD13 0.66 1.66 6 61:A:30:GLN:HG2 1:A:136:GLN:HA 0.66 1.65 8 11:A:136:GLN:NE2 1:A:136:GLN:H 0.66 1.87 8 1
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:59:TYR:CE1 1:A:71:ILE:HG23 0.65 2.26 8 11:A:13:ASN:CB 1:A:59:TYR:HB3 0.65 2.20 7 11:A:30:GLN:OE1 1:A:43:ALA:HA 0.65 1.92 3 11:A:80:TYR:CE1 1:A:108:ASN:HB2 0.65 2.26 11 21:A:54:PHE:CD2 1:A:72:LEU:HG 0.65 2.26 8 111:A:59:TYR:CD1 1:A:102:ILE:HG13 0.65 2.27 3 11:A:67:LYS:HB3 1:A:112:PHE:CD1 0.65 2.27 2 31:A:71:ILE:HD13 1:A:98:ILE:HG21 0.65 1.69 13 11:A:122:PHE:HB2 1:A:132:ILE:HB 0.65 1.69 5 141:A:133:ALA:HA 1:A:150:THR:HA 0.64 1.69 10 81:A:129:ASN:HA 1:A:144:GLY:CA 0.64 2.23 1 51:A:25:ASN:OD1 1:A:29:ASN:HA 0.64 1.92 2 31:A:133:ALA:O 1:A:140:VAL:HG13 0.64 1.92 6 61:A:80:TYR:CD1 1:A:93:LYS:HB3 0.64 2.27 11 31:A:45:LEU:CD1 1:A:48:LEU:HA 0.64 2.23 1 11:A:82:THR:HG23 1:A:93:LYS:CG 0.64 2.23 7 31:A:25:ASN:ND2 1:A:29:ASN:HA 0.64 2.08 11 31:A:71:ILE:HG21 1:A:98:ILE:HG22 0.64 1.68 1 21:A:129:ASN:HA 1:A:144:GLY:HA2 0.64 1.69 13 51:A:82:THR:CG2 1:A:91:LEU:HB2 0.64 2.23 11 101:A:59:TYR:CE2 1:A:69:THR:HG21 0.64 2.28 2 11:A:15:MET:HG2 1:A:60:LYS:HB2 0.63 1.68 13 21:A:82:THR:HG22 1:A:108:ASN:CB 0.63 2.24 1 31:A:14:PHE:HB3 1:A:100:LYS:HA 0.63 1.69 3 21:A:81:VAL:HG13 1:A:90:VAL:HG21 0.63 1.69 9 11:A:124:SER:HB3 1:A:127:HIS:O 0.63 1.92 14 91:A:135:LYS:HG3 1:A:139:TRP:O 0.63 1.94 1 21:A:15:MET:HB3 1:A:58:ALA:O 0.63 1.92 12 41:A:72:LEU:H 1:A:109:LEU:HD11 0.63 1.53 8 21:A:25:ASN:O 1:A:152:PHE:HA 0.63 1.93 6 81:A:82:THR:HB 1:A:93:LYS:HB2 0.63 1.69 12 101:A:26:ASP:HB3 1:A:134:THR:HB 0.63 1.70 5 21:A:26:ASP:CG 1:A:134:THR:HB 0.63 2.14 8 1
1:A:48:LEU:HD13 1:A:155:LEU:HB3 0.63 1.69 13 11:A:102:ILE:HD12 1:A:106:GLU:HB3 0.62 1.72 6 11:A:149:ILE:HD12 1:A:149:ILE:H 0.62 1.53 10 11:A:82:THR:OG1 1:A:108:ASN:HB3 0.62 1.94 3 101:A:78:GLN:HB3 1:A:96:PRO:HA 0.62 1.71 8 21:A:13:ASN:HB3 1:A:60:LYS:N 0.62 2.10 8 51:A:59:TYR:HE1 1:A:71:ILE:HG23 0.62 1.54 8 11:A:59:TYR:CE2 1:A:110:LEU:HD22 0.62 2.26 2 1
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:59:TYR:CE2 1:A:69:THR:HB 0.62 2.30 9 11:A:32:ILE:HG22 1:A:42:ALA:HB2 0.61 1.72 12 51:A:109:LEU:HG 1:A:109:LEU:O 0.61 1.95 9 71:A:120:ASN:HB2 1:A:152:PHE:CD1 0.61 2.30 5 31:A:93:LYS:HD2 1:A:108:ASN:HB2 0.61 1.71 4 11:A:112:PHE:CE1 1:A:125:VAL:HG23 0.61 2.30 2 21:A:86:GLU:HG3 1:A:144:GLY:H 0.61 1.56 8 51:A:59:TYR:OH 1:A:110:LEU:HD23 0.61 1.96 14 21:A:133:ALA:HB2 1:A:148:SER:HB3 0.61 1.71 10 31:A:45:LEU:HD11 1:A:155:LEU:HD12 0.61 1.72 1 11:A:82:THR:HG22 1:A:108:ASN:CG 0.61 2.15 7 21:A:47:ASN:HB3 1:A:50:GLU:HB2 0.61 1.73 12 11:A:24:LEU:HG 1:A:152:PHE:HD2 0.60 1.54 6 61:A:24:LEU:HG 1:A:152:PHE:CD2 0.60 2.31 5 61:A:13:ASN:HB3 1:A:59:TYR:HB2 0.60 1.73 8 11:A:123:THR:HA 1:A:131:PHE:CB 0.60 2.23 9 11:A:79:LEU:HD21 1:A:92:LEU:HB3 0.60 1.72 8 11:A:80:TYR:OH 1:A:108:ASN:HB2 0.60 1.97 11 11:A:30:GLN:HG2 1:A:42:ALA:CB 0.60 2.26 11 21:A:18:ILE:HB 1:A:56:MET:O 0.60 1.97 4 111:A:28:LEU:CB 1:A:30:GLN:HE22 0.60 2.10 7 21:A:59:TYR:C 1:A:59:TYR:CD1 0.60 2.76 2 2
1:A:84:GLN:HG3 1:A:85:ASP:N 0.60 2.12 11 11:A:109:LEU:O 1:A:109:LEU:HG 0.59 1.95 11 41:A:20:TYR:HB3 1:A:55:ASP:OD1 0.59 1.97 11 51:A:28:LEU:CD1 1:A:149:ILE:HG13 0.59 2.26 8 11:A:80:TYR:CD2 1:A:109:LEU:HD13 0.59 2.32 11 11:A:25:ASN:OD1 1:A:153:GLN:HB2 0.59 1.97 10 11:A:22:PHE:HB2 1:A:154:ILE:HG13 0.59 1.74 7 11:A:30:GLN:HG2 1:A:42:ALA:HB1 0.59 1.72 7 21:A:135:LYS:HD3 1:A:138:TYR:HB2 0.59 1.73 9 11:A:23:ILE:HG21 1:A:48:LEU:O 0.59 1.97 1 61:A:13:ASN:HB2 1:A:59:TYR:HB2 0.59 1.72 6 21:A:24:LEU:HD13 1:A:54:PHE:CE1 0.59 2.32 1 11:A:20:TYR:HB2 1:A:55:ASP:OD1 0.59 1.98 1 21:A:18:ILE:HG22 1:A:19:LYS:HG3 0.59 1.74 7 21:A:133:ALA:CA 1:A:150:THR:HG22 0.59 2.28 9 51:A:31:SER:OG 1:A:45:LEU:HB2 0.58 1.98 9 2
1:A:102:ILE:HG13 1:A:106:GLU:HB2 0.58 1.74 9 11:A:71:ILE:HG21 1:A:98:ILE:HG23 0.58 1.75 11 11:A:32:ILE:HD13 1:A:140:VAL:HG21 0.58 1.73 6 1
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:28:LEU:HB3 1:A:30:GLN:HE22 0.58 1.58 7 21:A:28:LEU:CD2 1:A:149:ILE:HG13 0.58 2.28 12 71:A:45:LEU:HD12 1:A:50:GLU:HB3 0.58 1.76 12 11:A:80:TYR:CD2 1:A:95:MET:HB3 0.58 2.33 14 41:A:67:LYS:HB2 1:A:112:PHE:CD1 0.58 2.34 1 41:A:13:ASN:HB2 1:A:60:LYS:N 0.58 2.14 10 31:A:99:PRO:HG2 1:A:102:ILE:HG12 0.58 1.75 13 11:A:32:ILE:HB 1:A:40:LEU:CD2 0.57 2.28 3 41:A:122:PHE:HZ 1:A:152:PHE:HB3 0.57 1.59 9 11:A:112:PHE:HB2 1:A:123:THR:HB 0.57 1.76 10 21:A:32:ILE:HD11 1:A:40:LEU:HD23 0.57 1.74 5 31:A:121:TYR:HB3 1:A:131:PHE:CE1 0.57 2.34 3 51:A:119:LYS:HE3 1:A:121:TYR:CZ 0.57 2.34 10 11:A:23:ILE:HB 1:A:155:LEU:CB 0.57 2.29 10 21:A:80:TYR:O 1:A:93:LYS:HG3 0.57 2.00 1 11:A:48:LEU:CB 1:A:157:ASN:HA 0.57 2.29 7 31:A:13:ASN:ND2 1:A:102:ILE:HB 0.57 2.13 9 21:A:102:ILE:CG2 1:A:106:GLU:HB2 0.57 2.25 1 21:A:80:TYR:HD2 1:A:109:LEU:HD22 0.57 1.59 9 31:A:136:GLN:HA 1:A:136:GLN:OE1 0.57 1.98 3 11:A:22:PHE:HB2 1:A:154:ILE:HG23 0.57 1.75 13 11:A:89:PRO:HA 1:A:141:CYS:CA 0.57 2.27 12 21:A:80:TYR:HB3 1:A:109:LEU:HD13 0.57 1.74 7 51:A:18:ILE:HD11 1:A:58:ALA:HB2 0.57 1.75 11 51:A:82:THR:HG21 1:A:91:LEU:HB2 0.57 1.77 11 101:A:81:VAL:H 1:A:109:LEU:HD13 0.57 1.59 5 3
1:A:109:LEU:HD12 1:A:111:PHE:CE2 0.57 2.35 5 31:A:133:ALA:HA 1:A:150:THR:HG22 0.57 1.75 9 41:A:86:GLU:HG2 1:A:87:ASP:N 0.57 2.15 1 61:A:130:LEU:HG 1:A:142:LEU:HD21 0.57 1.76 2 71:A:60:LYS:HE2 1:A:68:ILE:HD12 0.57 1.74 10 11:A:79:LEU:HD11 1:A:92:LEU:HB3 0.57 1.76 10 21:A:28:LEU:HB3 1:A:136:GLN:HE21 0.56 1.59 5 51:A:57:GLY:H 1:A:71:ILE:HG22 0.56 1.59 14 1
1:A:26:ASP:OD1 1:A:30:GLN:HG2 0.56 2.00 12 11:A:80:TYR:HD1 1:A:93:LYS:HB3 0.56 1.57 11 11:A:107:THR:O 1:A:110:LEU:HG 0.56 2.01 2 101:A:13:ASN:CG 1:A:59:TYR:HB2 0.56 2.21 6 11:A:48:LEU:HB3 1:A:157:ASN:HA 0.56 1.76 12 11:A:111:PHE:CE2 1:A:132:ILE:HG13 0.56 2.36 13 11:A:28:LEU:HD21 1:A:149:ILE:HG12 0.56 1.78 4 2
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:59:TYR:HD2 1:A:71:ILE:HD13 0.56 1.60 11 21:A:81:VAL:HG13 1:A:90:VAL:HG11 0.56 1.76 8 31:A:28:LEU:HD13 1:A:136:GLN:CG 0.56 2.30 4 11:A:13:ASN:HD22 1:A:102:ILE:HB 0.56 1.60 13 11:A:131:PHE:CE1 1:A:150:THR:CG2 0.56 2.84 9 11:A:102:ILE:HD12 1:A:110:LEU:HD21 0.56 1.76 10 21:A:25:ASN:O 1:A:153:GLN:HG2 0.56 2.01 11 41:A:31:SER:OG 1:A:45:LEU:HB3 0.55 2.01 6 11:A:119:LYS:HA 1:A:153:GLN:HG2 0.55 1.77 10 21:A:127:HIS:HB3 1:A:130:LEU:HD13 0.55 1.77 11 11:A:132:ILE:HG22 1:A:152:PHE:HE2 0.55 1.61 1 31:A:99:PRO:HB2 1:A:102:ILE:HG12 0.55 1.76 1 11:A:23:ILE:CD1 1:A:49:ASP:HA 0.55 2.31 3 81:A:49:ASP:HB2 1:A:157:ASN:CB 0.55 2.31 14 31:A:80:TYR:CE2 1:A:109:LEU:HD22 0.55 2.37 11 11:A:30:GLN:HB3 1:A:42:ALA:HB1 0.55 1.78 9 31:A:13:ASN:HA 1:A:60:LYS:O 0.55 2.02 9 31:A:67:LYS:HB3 1:A:112:PHE:CE1 0.55 2.36 2 21:A:20:TYR:HD2 1:A:56:MET:N 0.55 1.99 14 1
1:A:115:THR:HG22 1:A:120:ASN:OD1 0.55 2.02 11 11:A:121:TYR:HB3 1:A:131:PHE:CZ 0.55 2.37 3 51:A:31:SER:HB3 1:A:51:ALA:CB 0.55 2.27 6 11:A:45:LEU:HD21 1:A:48:LEU:HA 0.55 1.79 12 11:A:34:ARG:HA 1:A:40:LEU:CD1 0.55 2.32 7 81:A:30:GLN:HA 1:A:44:ALA:HA 0.55 1.78 11 51:A:49:ASP:CB 1:A:157:ASN:HB2 0.55 2.32 9 31:A:122:PHE:CZ 1:A:152:PHE:HB3 0.54 2.37 9 11:A:68:ILE:H 1:A:68:ILE:HD13 0.54 1.61 4 1
1:A:79:LEU:HD13 1:A:92:LEU:HD13 0.54 1.79 5 21:A:13:ASN:HB2 1:A:100:LYS:O 0.54 2.02 1 11:A:23:ILE:HG12 1:A:49:ASP:HA 0.54 1.78 8 11:A:81:VAL:HB 1:A:109:LEU:CD1 0.54 2.31 14 21:A:19:LYS:HB3 1:A:22:PHE:CE2 0.54 2.37 5 31:A:69:THR:HG23 1:A:110:LEU:HA 0.54 1.79 14 21:A:13:ASN:N 1:A:101:THR:HA 0.54 2.18 12 5
1:A:123:THR:HG22 1:A:128:PRO:HA 0.54 1.79 2 51:A:32:ILE:HG13 1:A:32:ILE:O 0.54 2.03 1 51:A:82:THR:CA 1:A:108:ASN:HB3 0.54 2.32 1 41:A:37:ASP:HA 1:A:79:LEU:HD21 0.54 1.78 2 11:A:13:ASN:HB3 1:A:60:LYS:O 0.54 2.03 3 11:A:83:ALA:CB 1:A:130:LEU:HD23 0.54 2.32 2 3
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Page 20 Full wwPDB NMR Structure Validation Report 2KKI
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:28:LEU:HD12 1:A:136:GLN:NE2 0.54 2.17 8 11:A:28:LEU:HB3 1:A:136:GLN:OE1 0.54 2.02 3 11:A:30:GLN:HG3 1:A:136:GLN:CB 0.54 2.33 6 11:A:110:LEU:HB3 1:A:125:VAL:HG12 0.54 1.79 10 21:A:71:ILE:HG21 1:A:98:ILE:HD12 0.54 1.80 11 11:A:28:LEU:HG 1:A:149:ILE:HG13 0.54 1.80 5 11:A:24:LEU:HD23 1:A:32:ILE:HD11 0.53 1.80 12 11:A:127:HIS:O 1:A:130:LEU:HG 0.53 2.04 6 1
1:A:20:TYR:CE2 1:A:56:MET:HG3 0.53 2.38 14 11:A:25:ASN:OD1 1:A:45:LEU:HD22 0.53 2.03 1 11:A:27:ALA:H 1:A:151:ASP:CB 0.53 2.15 10 6
1:A:30:GLN:OE1 1:A:136:GLN:HG2 0.53 2.04 2 11:A:23:ILE:HD13 1:A:53:LYS:HG2 0.53 1.80 3 61:A:25:ASN:HD21 1:A:45:LEU:HD12 0.53 1.64 6 11:A:28:LEU:HD11 1:A:149:ILE:CD1 0.53 2.33 10 11:A:34:ARG:HB3 1:A:52:VAL:HG11 0.52 1.81 3 11:A:45:LEU:HG 1:A:48:LEU:O 0.52 2.05 14 31:A:115:THR:HA 1:A:120:ASN:HD22 0.52 1.64 14 11:A:32:ILE:O 1:A:32:ILE:HG13 0.52 2.05 3 11:A:45:LEU:H 1:A:45:LEU:CD1 0.52 2.17 10 1
1:A:16:ARG:HD2 1:A:58:ALA:HB3 0.52 1.81 5 31:A:59:TYR:HE2 1:A:71:ILE:HG12 0.52 1.64 5 11:A:26:ASP:OD1 1:A:26:ASP:N 0.52 2.42 8 11:A:80:TYR:CE2 1:A:109:LEU:CB 0.52 2.93 5 11:A:69:THR:HG21 1:A:110:LEU:HD22 0.52 1.80 8 11:A:110:LEU:CB 1:A:125:VAL:HG12 0.52 2.35 2 11:A:71:ILE:CD1 1:A:98:ILE:HG23 0.52 2.35 7 11:A:30:GLN:HE21 1:A:136:GLN:N 0.52 2.02 8 11:A:30:GLN:HB2 1:A:43:ALA:CA 0.52 2.35 7 11:A:45:LEU:CD1 1:A:50:GLU:HB3 0.52 2.33 12 51:A:45:LEU:CD2 1:A:48:LEU:HA 0.52 2.35 12 11:A:135:LYS:HG2 1:A:138:TYR:HB2 0.52 1.81 10 21:A:45:LEU:HD21 1:A:48:LEU:O 0.52 2.06 12 11:A:48:LEU:HD13 1:A:156:GLU:O 0.51 2.05 7 61:A:89:PRO:CA 1:A:141:CYS:HA 0.51 2.32 3 11:A:49:ASP:HB3 1:A:157:ASN:OD1 0.51 2.05 13 4
1:A:109:LEU:HD12 1:A:111:PHE:HE2 0.51 1.65 2 21:A:27:ALA:N 1:A:151:ASP:HB2 0.51 2.21 10 1
1:A:80:TYR:CE1 1:A:93:LYS:HB3 0.51 2.40 10 21:A:70:VAL:HB 1:A:111:PHE:CE1 0.51 2.40 4 1
1:A:28:LEU:HD12 1:A:136:GLN:CD 0.51 2.25 8 1Continued on next page...
Page 21 Full wwPDB NMR Structure Validation Report 2KKI
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:30:GLN:HE21 1:A:136:GLN:CA 0.51 2.19 8 11:A:18:ILE:HG22 1:A:19:LYS:H 0.51 1.64 14 11:A:71:ILE:HD12 1:A:98:ILE:HG23 0.51 1.83 7 11:A:26:ASP:CB 1:A:134:THR:HB 0.51 2.35 5 2
1:A:81:VAL:HG13 1:A:90:VAL:CG1 0.51 2.35 14 21:A:81:VAL:HG13 1:A:90:VAL:CG2 0.51 2.36 9 11:A:18:ILE:HG13 1:A:57:GLY:HA2 0.51 1.82 14 31:A:68:ILE:HD13 1:A:68:ILE:H 0.51 1.66 11 11:A:80:TYR:HE2 1:A:109:LEU:HD22 0.51 1.64 11 11:A:15:MET:HB3 1:A:58:ALA:C 0.50 2.26 12 31:A:120:ASN:HB2 1:A:152:PHE:HD1 0.50 1.66 5 11:A:23:ILE:HG13 1:A:48:LEU:O 0.50 2.07 12 11:A:26:ASP:HB3 1:A:134:THR:CB 0.50 2.36 5 31:A:79:LEU:HD11 1:A:92:LEU:HD22 0.50 1.83 8 11:A:158:GLN:HA 1:A:158:GLN:HE21 0.50 1.67 11 11:A:82:THR:HG22 1:A:91:LEU:O 0.50 2.06 10 61:A:45:LEU:HG 1:A:155:LEU:CD1 0.50 2.34 2 21:A:74:ILE:HG22 1:A:76:LYS:H 0.50 1.67 4 1
1:A:107:THR:HG23 1:A:110:LEU:HD11 0.50 1.82 8 11:A:80:TYR:CB 1:A:93:LYS:HE2 0.50 2.36 1 11:A:48:LEU:HD12 1:A:156:GLU:O 0.50 2.06 13 11:A:24:LEU:HD22 1:A:32:ILE:CG2 0.50 2.36 13 41:A:82:THR:OG1 1:A:91:LEU:HB2 0.50 2.07 6 41:A:131:PHE:O 1:A:142:LEU:HD12 0.50 2.06 6 13
1:A:45:LEU:HD11 1:A:48:LEU:O 0.50 2.07 12 11:A:28:LEU:CG 1:A:149:ILE:HG13 0.50 2.36 5 71:A:13:ASN:N 1:A:102:ILE:H 0.50 2.05 12 21:A:70:VAL:HB 1:A:111:PHE:CZ 0.50 2.42 4 11:A:86:GLU:CG 1:A:87:ASP:H 0.50 2.17 5 41:A:30:GLN:HB2 1:A:43:ALA:N 0.50 2.22 13 11:A:22:PHE:HZ 1:A:56:MET:HG3 0.49 1.66 7 11:A:42:ALA:HB3 1:A:135:LYS:O 0.49 2.07 8 61:A:70:VAL:HG22 1:A:111:PHE:CE2 0.49 2.41 9 11:A:28:LEU:HB2 1:A:30:GLN:OE1 0.49 2.07 8 21:A:59:TYR:C 1:A:59:TYR:HD1 0.49 2.10 2 1
1:A:49:ASP:HB2 1:A:157:ASN:HB3 0.49 1.84 7 11:A:131:PHE:HE1 1:A:150:THR:HG21 0.49 1.63 9 11:A:78:GLN:NE2 1:A:78:GLN:H 0.49 2.05 12 11:A:131:PHE:CB 1:A:144:GLY:HA2 0.49 2.37 3 11:A:112:PHE:CD2 1:A:123:THR:HB 0.49 2.43 2 21:A:15:MET:HB2 1:A:59:TYR:C 0.49 2.27 7 1
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Page 22 Full wwPDB NMR Structure Validation Report 2KKI
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:111:PHE:CE1 1:A:132:ILE:HG13 0.49 2.43 10 11:A:132:ILE:HG22 1:A:152:PHE:HZ 0.49 1.68 4 11:A:25:ASN:HD21 1:A:45:LEU:HD13 0.49 1.66 1 11:A:48:LEU:HD22 1:A:155:LEU:HD13 0.49 1.84 11 11:A:135:LYS:HE2 1:A:141:CYS:HB3 0.49 1.85 3 11:A:28:LEU:CD2 1:A:149:ILE:HG12 0.49 2.38 4 41:A:74:ILE:HD13 1:A:74:ILE:H 0.49 1.66 6 21:A:131:PHE:O 1:A:142:LEU:HA 0.49 2.07 2 41:A:33:ILE:HG22 1:A:51:ALA:CA 0.49 2.30 9 11:A:81:VAL:HG11 1:A:111:PHE:HZ 0.49 1.68 8 11:A:34:ARG:HG3 1:A:52:VAL:HG11 0.49 1.84 8 11:A:129:ASN:CA 1:A:144:GLY:HA2 0.49 2.38 13 31:A:29:ASN:HD22 1:A:29:ASN:N 0.49 2.06 7 11:A:89:PRO:HB3 1:A:139:TRP:CD1 0.49 2.42 1 11:A:14:PHE:HB3 1:A:100:LYS:CA 0.49 2.36 3 11:A:13:ASN:H 1:A:101:THR:CA 0.49 2.20 6 21:A:13:ASN:O 1:A:59:TYR:HB3 0.49 2.07 5 2
1:A:102:ILE:HG23 1:A:106:GLU:CB 0.49 2.32 1 11:A:109:LEU:HD12 1:A:111:PHE:HE1 0.49 1.66 13 1
1:A:37:ASP:O 1:A:92:LEU:HD11 0.49 2.07 13 11:A:33:ILE:HG23 1:A:51:ALA:HA 0.49 1.85 13 11:A:15:MET:HG2 1:A:60:LYS:CG 0.48 2.38 7 11:A:45:LEU:HD21 1:A:50:GLU:HB3 0.48 1.85 3 21:A:74:ILE:HG12 1:A:76:LYS:H 0.48 1.68 3 11:A:69:THR:OG1 1:A:110:LEU:HA 0.48 2.09 6 41:A:80:TYR:C 1:A:80:TYR:CD1 0.48 2.86 12 2
1:A:149:ILE:HD12 1:A:149:ILE:N 0.48 2.24 10 21:A:74:ILE:HG13 1:A:76:LYS:H 0.48 1.68 13 11:A:120:ASN:HB2 1:A:152:PHE:CE1 0.48 2.44 12 21:A:82:THR:HG23 1:A:93:LYS:CB 0.48 2.39 7 41:A:71:ILE:HG13 1:A:109:LEU:CD2 0.48 2.38 10 31:A:71:ILE:CG2 1:A:109:LEU:HD21 0.48 2.28 6 41:A:13:ASN:O 1:A:13:ASN:ND2 0.48 2.47 6 3
1:A:25:ASN:ND2 1:A:45:LEU:HD12 0.48 2.24 6 11:A:69:THR:HG23 1:A:111:PHE:H 0.48 1.69 2 11:A:71:ILE:HD11 1:A:99:PRO:HD2 0.48 1.86 7 11:A:69:THR:OG1 1:A:125:VAL:HG11 0.48 2.09 2 11:A:133:ALA:HB1 1:A:148:SER:CB 0.47 2.37 5 21:A:80:TYR:HE1 1:A:108:ASN:HB2 0.47 1.64 11 11:A:85:ASP:HA 1:A:130:LEU:CD2 0.47 2.34 6 21:A:26:ASP:OD1 1:A:30:GLN:N 0.47 2.44 6 3
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Page 23 Full wwPDB NMR Structure Validation Report 2KKI
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:69:THR:HA 1:A:111:PHE:O 0.47 2.09 10 11:A:48:LEU:HB3 1:A:156:GLU:O 0.47 2.09 12 21:A:103:THR:O 1:A:105:SER:N 0.47 2.46 3 41:A:24:LEU:HB3 1:A:32:ILE:HG22 0.47 1.85 4 31:A:59:TYR:CD1 1:A:102:ILE:HD12 0.47 2.43 1 11:A:93:LYS:NZ 1:A:109:LEU:HB2 0.47 2.24 1 11:A:23:ILE:HG13 1:A:49:ASP:HA 0.47 1.86 2 11:A:72:LEU:HD23 1:A:81:VAL:HG21 0.47 1.86 1 41:A:13:ASN:CG 1:A:102:ILE:HB 0.47 2.30 11 31:A:102:ILE:CD1 1:A:110:LEU:HD21 0.47 2.39 7 11:A:93:LYS:HG3 1:A:93:LYS:O 0.47 2.09 7 11:A:30:GLN:CD 1:A:136:GLN:HA 0.47 2.30 13 21:A:13:ASN:HB2 1:A:60:LYS:H 0.47 1.69 6 11:A:30:GLN:HG3 1:A:136:GLN:HB3 0.47 1.86 6 11:A:18:ILE:HG22 1:A:19:LYS:N 0.47 2.24 14 31:A:25:ASN:ND2 1:A:45:LEU:HD13 0.47 2.24 1 11:A:82:THR:HG22 1:A:108:ASN:ND2 0.47 2.25 1 11:A:92:LEU:HD12 1:A:92:LEU:O 0.47 2.08 13 11:A:131:PHE:HE1 1:A:150:THR:CB 0.47 2.23 9 11:A:131:PHE:HE1 1:A:150:THR:CG2 0.47 2.21 9 11:A:13:ASN:HB3 1:A:102:ILE:HG22 0.47 1.87 9 11:A:149:ILE:N 1:A:149:ILE:HD12 0.47 2.25 9 21:A:45:LEU:H 1:A:45:LEU:HD13 0.47 1.70 10 1
1:A:107:THR:HA 1:A:110:LEU:HD21 0.47 1.87 2 11:A:112:PHE:CD1 1:A:125:VAL:HG23 0.47 2.44 2 11:A:30:GLN:HG3 1:A:43:ALA:HA 0.47 1.87 9 11:A:13:ASN:HB2 1:A:59:TYR:CB 0.47 2.40 6 11:A:124:SER:HB2 1:A:127:HIS:O 0.47 2.10 2 21:A:45:LEU:HD12 1:A:48:LEU:N 0.46 2.25 3 21:A:149:ILE:HG22 1:A:151:ASP:OD2 0.46 2.10 10 11:A:53:LYS:HG3 1:A:75:SER:OG 0.46 2.10 8 11:A:122:PHE:O 1:A:131:PHE:HB2 0.46 2.10 9 1
1:A:110:LEU:HD21 1:A:126:ALA:HB2 0.46 1.87 1 31:A:30:GLN:HB2 1:A:42:ALA:HB1 0.46 1.87 12 21:A:111:PHE:CD2 1:A:132:ILE:HG13 0.46 2.45 13 11:A:64:ASP:HB3 1:A:67:LYS:O 0.46 2.11 2 21:A:45:LEU:HD12 1:A:48:LEU:CA 0.46 2.30 1 11:A:82:THR:HA 1:A:108:ASN:CB 0.46 2.40 14 31:A:136:GLN:N 1:A:136:GLN:NE2 0.46 2.61 8 11:A:95:MET:HG2 1:A:106:GLU:HG3 0.46 1.86 8 11:A:80:TYR:HB2 1:A:93:LYS:O 0.46 2.10 14 2
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Page 24 Full wwPDB NMR Structure Validation Report 2KKI
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:109:LEU:O 1:A:109:LEU:CG 0.46 2.62 11 11:A:73:ARG:HD3 1:A:98:ILE:HD11 0.46 1.86 11 11:A:26:ASP:HB3 1:A:151:ASP:O 0.46 2.11 7 41:A:94:GLU:O 1:A:94:GLU:HG2 0.46 2.11 3 1
1:A:24:LEU:HD22 1:A:32:ILE:HG12 0.46 1.87 10 11:A:115:THR:HA 1:A:120:ASN:ND2 0.46 2.26 14 11:A:19:LYS:HE3 1:A:22:PHE:CE2 0.46 2.46 1 21:A:100:LYS:HD3 1:A:100:LYS:N 0.46 2.21 5 11:A:28:LEU:HD23 1:A:28:LEU:N 0.46 2.26 8 11:A:19:LYS:HE2 1:A:154:ILE:HD12 0.46 1.87 1 11:A:80:TYR:C 1:A:80:TYR:HD1 0.46 2.15 12 1
1:A:59:TYR:CE2 1:A:69:THR:CB 0.46 2.99 9 11:A:112:PHE:O 1:A:122:PHE:HA 0.46 2.10 1 11:A:24:LEU:HG 1:A:152:PHE:CD1 0.46 2.46 1 11:A:93:LYS:HD2 1:A:108:ASN:CB 0.45 2.41 4 11:A:33:ILE:HG12 1:A:51:ALA:CA 0.45 2.40 8 11:A:58:ALA:HB2 1:A:70:VAL:HG12 0.45 1.87 8 11:A:120:ASN:HB3 1:A:152:PHE:HD1 0.45 1.70 2 11:A:45:LEU:HD23 1:A:155:LEU:HD12 0.45 1.87 12 11:A:25:ASN:HD21 1:A:29:ASN:HA 0.45 1.69 11 11:A:131:PHE:HD1 1:A:132:ILE:N 0.45 2.09 10 11:A:59:TYR:CZ 1:A:69:THR:HG21 0.45 2.46 4 1
1:A:111:PHE:CD1 1:A:132:ILE:HG13 0.45 2.46 3 11:A:52:VAL:HG23 1:A:54:PHE:CE1 0.45 2.46 8 11:A:45:LEU:CD1 1:A:155:LEU:HD12 0.45 2.41 1 11:A:93:LYS:HZ1 1:A:109:LEU:HB2 0.45 1.70 7 11:A:72:LEU:HD22 1:A:81:VAL:HG23 0.45 1.87 4 11:A:99:PRO:HB2 1:A:102:ILE:CG1 0.45 2.42 1 11:A:49:ASP:OD1 1:A:157:ASN:HB2 0.45 2.12 12 11:A:86:GLU:HA 1:A:143:ALA:HA 0.45 1.88 7 31:A:127:HIS:HB2 1:A:130:LEU:HD22 0.45 1.88 3 31:A:20:TYR:HB3 1:A:55:ASP:HB3 0.45 1.87 3 11:A:121:TYR:HA 1:A:150:THR:O 0.45 2.11 9 21:A:19:LYS:HB3 1:A:22:PHE:HE2 0.45 1.69 5 31:A:57:GLY:N 1:A:71:ILE:HG13 0.45 2.23 13 1
1:A:32:ILE:HD11 1:A:40:LEU:HB3 0.45 1.87 9 11:A:80:TYR:HD2 1:A:109:LEU:CD2 0.45 2.25 2 21:A:111:PHE:HB2 1:A:122:PHE:HB3 0.45 1.88 4 11:A:25:ASN:O 1:A:153:GLN:N 0.45 2.49 7 5
1:A:15:MET:HB3 1:A:58:ALA:HB3 0.45 1.89 7 11:A:120:ASN:HB3 1:A:152:PHE:CE1 0.45 2.47 9 4
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Page 25 Full wwPDB NMR Structure Validation Report 2KKI
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:15:MET:HB2 1:A:60:LYS:HB2 0.45 1.88 1 11:A:79:LEU:HD11 1:A:92:LEU:CB 0.45 2.41 10 11:A:72:LEU:O 1:A:109:LEU:HD11 0.45 2.13 5 21:A:13:ASN:CB 1:A:60:LYS:O 0.44 2.65 3 11:A:13:ASN:H 1:A:101:THR:HA 0.44 1.72 8 2
1:A:59:TYR:CE2 1:A:71:ILE:HG12 0.44 2.47 5 11:A:78:GLN:CB 1:A:96:PRO:HA 0.44 2.39 8 11:A:32:ILE:HG23 1:A:54:PHE:HE1 0.44 1.70 13 11:A:33:ILE:O 1:A:40:LEU:HG 0.44 2.13 14 4
1:A:115:THR:HA 1:A:120:ASN:OD1 0.44 2.12 5 11:A:86:GLU:O 1:A:88:GLN:N 0.44 2.50 3 91:A:93:LYS:O 1:A:93:LYS:HG3 0.44 2.13 6 2
1:A:30:GLN:OE1 1:A:134:THR:HG22 0.44 2.12 11 11:A:71:ILE:CD1 1:A:99:PRO:HD2 0.44 2.41 7 21:A:16:ARG:HD3 1:A:16:ARG:O 0.44 2.13 5 11:A:136:GLN:H 1:A:136:GLN:CD 0.44 2.14 8 11:A:32:ILE:HD13 1:A:152:PHE:CE1 0.44 2.47 8 11:A:109:LEU:HD12 1:A:111:PHE:CD2 0.44 2.47 14 11:A:33:ILE:HG12 1:A:51:ALA:CB 0.44 2.42 7 21:A:132:ILE:HG22 1:A:152:PHE:CE2 0.44 2.45 1 21:A:32:ILE:HD13 1:A:140:VAL:CG2 0.44 2.40 6 11:A:32:ILE:CD1 1:A:40:LEU:HD23 0.44 2.42 5 11:A:94:GLU:O 1:A:94:GLU:HG3 0.44 2.13 1 1
1:A:112:PHE:HB3 1:A:123:THR:HB 0.44 1.90 7 21:A:26:ASP:N 1:A:26:ASP:OD1 0.44 2.45 11 2
1:A:111:PHE:CE1 1:A:132:ILE:HG12 0.44 2.48 14 11:A:23:ILE:HB 1:A:155:LEU:O 0.44 2.13 7 1
1:A:45:LEU:HD23 1:A:48:LEU:HA 0.44 1.88 6 31:A:74:ILE:HD11 1:A:79:LEU:HB2 0.44 1.90 1 11:A:20:TYR:CG 1:A:55:ASP:HA 0.44 2.43 14 11:A:80:TYR:CB 1:A:93:LYS:HE3 0.44 2.43 7 11:A:26:ASP:HA 1:A:151:ASP:O 0.44 2.12 9 21:A:98:ILE:O 1:A:98:ILE:HD12 0.44 2.12 10 1
1:A:28:LEU:HG 1:A:149:ILE:CG1 0.44 2.42 5 11:A:109:LEU:HD12 1:A:111:PHE:CE1 0.44 2.47 13 11:A:102:ILE:CD1 1:A:106:GLU:HB3 0.44 2.43 6 11:A:23:ILE:CG1 1:A:49:ASP:HA 0.44 2.43 8 11:A:57:GLY:N 1:A:71:ILE:HG22 0.44 2.27 14 11:A:59:TYR:OH 1:A:71:ILE:HD11 0.43 2.13 7 11:A:30:GLN:NE2 1:A:136:GLN:HE21 0.43 2.11 11 21:A:111:PHE:CE1 1:A:132:ILE:HD11 0.43 2.47 6 1
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:33:ILE:HA 1:A:52:VAL:HG22 0.43 1.89 12 11:A:26:ASP:CB 1:A:134:THR:OG1 0.43 2.66 13 21:A:15:MET:HB3 1:A:58:ALA:CB 0.43 2.43 7 11:A:80:TYR:CD1 1:A:80:TYR:C 0.43 2.91 10 11:A:30:GLN:NE2 1:A:136:GLN:NE2 0.43 2.67 7 11:A:15:MET:HG2 1:A:60:LYS:CB 0.43 2.43 7 11:A:139:TRP:CD1 1:A:140:VAL:N 0.43 2.86 3 11:A:25:ASN:HB2 1:A:155:LEU:CD1 0.43 2.44 2 11:A:30:GLN:HB2 1:A:44:ALA:N 0.43 2.28 11 11:A:13:ASN:CG 1:A:60:LYS:HB3 0.43 2.34 3 1
1:A:131:PHE:HD1 1:A:132:ILE:H 0.43 1.54 10 11:A:119:LYS:CA 1:A:152:PHE:O 0.43 2.65 5 11:A:13:ASN:HA 1:A:100:LYS:O 0.43 2.13 2 21:A:80:TYR:OH 1:A:97:GLU:O 0.43 2.37 14 11:A:45:LEU:HD22 1:A:45:LEU:C 0.43 2.33 2 11:A:32:ILE:HD13 1:A:140:VAL:HG23 0.43 1.90 11 11:A:80:TYR:HB2 1:A:109:LEU:HD13 0.43 1.91 10 11:A:124:SER:HB3 1:A:130:LEU:HB2 0.43 1.91 7 21:A:95:MET:SD 1:A:96:PRO:HD2 0.43 2.54 12 21:A:110:LEU:HB3 1:A:125:VAL:CG1 0.43 2.43 10 21:A:56:MET:HG2 1:A:71:ILE:O 0.43 2.14 14 11:A:54:PHE:CA 1:A:73:ARG:O 0.43 2.66 14 11:A:15:MET:HB2 1:A:59:TYR:CA 0.43 2.43 11 11:A:15:MET:SD 1:A:16:ARG:HD2 0.42 2.54 7 11:A:135:LYS:HE2 1:A:141:CYS:CB 0.42 2.43 3 11:A:28:LEU:HB3 1:A:136:GLN:CD 0.42 2.35 3 11:A:28:LEU:HG 1:A:149:ILE:CG2 0.42 2.38 8 11:A:74:ILE:HD11 1:A:77:THR:OG1 0.42 2.14 8 11:A:86:GLU:CD 1:A:144:GLY:H 0.42 2.18 4 11:A:141:CYS:SG 1:A:142:LEU:N 0.42 2.91 10 41:A:82:THR:O 1:A:90:VAL:HG23 0.42 2.15 9 11:A:134:THR:O 1:A:149:ILE:HB 0.42 2.14 8 11:A:73:ARG:HG3 1:A:73:ARG:O 0.42 2.14 8 11:A:90:VAL:HG12 1:A:142:LEU:HD13 0.42 1.90 2 11:A:69:THR:HG22 1:A:110:LEU:HB2 0.42 1.89 9 11:A:34:ARG:HA 1:A:40:LEU:HD12 0.42 1.92 4 11:A:13:ASN:O 1:A:59:TYR:HB2 0.42 2.14 14 11:A:102:ILE:O 1:A:102:ILE:HG23 0.42 2.14 11 3
1:A:73:ARG:HB2 1:A:80:TYR:CE1 0.42 2.50 4 11:A:13:ASN:HB3 1:A:60:LYS:H 0.42 1.75 8 11:A:34:ARG:HG2 1:A:40:LEU:HD12 0.42 1.92 8 1
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:131:PHE:HB3 1:A:144:GLY:HA2 0.42 1.90 3 11:A:30:GLN:NE2 1:A:44:ALA:HB2 0.42 2.30 10 11:A:30:GLN:HE21 1:A:136:GLN:HA 0.42 1.74 8 11:A:123:THR:HA 1:A:131:PHE:HD1 0.42 1.74 4 11:A:120:ASN:N 1:A:152:PHE:O 0.42 2.53 10 1
1:A:77:THR:HG23 1:A:79:LEU:HG 0.42 1.91 5 11:A:23:ILE:HD13 1:A:155:LEU:O 0.42 2.15 8 11:A:56:MET:HE3 1:A:70:VAL:HG21 0.42 1.91 8 11:A:112:PHE:CE1 1:A:125:VAL:CG2 0.42 3.01 2 11:A:13:ASN:H 1:A:102:ILE:N 0.42 2.13 12 11:A:119:LYS:C 1:A:120:ASN:HD22 0.42 2.18 11 1
1:A:23:ILE:HD11 1:A:49:ASP:OD2 0.41 2.15 7 11:A:18:ILE:HB 1:A:56:MET:HG3 0.41 1.91 10 11:A:28:LEU:HG 1:A:149:ILE:HG12 0.41 1.92 3 11:A:86:GLU:CG 1:A:87:ASP:N 0.41 2.79 3 11:A:116:HIS:O 1:A:119:LYS:HG2 0.41 2.15 14 1
1:A:20:TYR:CD2 1:A:56:MET:N 0.41 2.86 14 11:A:74:ILE:HG13 1:A:77:THR:O 0.41 2.14 9 11:A:26:ASP:O 1:A:29:ASN:HA 0.41 2.15 10 1
1:A:55:ASP:OD2 1:A:73:ARG:HD3 0.41 2.16 4 11:A:34:ARG:HB2 1:A:52:VAL:HG11 0.41 1.91 7 11:A:80:TYR:HB3 1:A:93:LYS:HE2 0.41 1.90 1 11:A:102:ILE:HD11 1:A:106:GLU:HB2 0.41 1.92 3 11:A:110:LEU:C 1:A:111:PHE:HD1 0.41 2.18 8 11:A:20:TYR:CE1 1:A:22:PHE:HB2 0.41 2.51 14 11:A:26:ASP:CG 1:A:28:LEU:HB2 0.41 2.36 2 11:A:22:PHE:CB 1:A:154:ILE:HG23 0.41 2.43 13 11:A:23:ILE:N 1:A:23:ILE:HD12 0.41 2.31 8 1
1:A:13:ASN:HB2 1:A:102:ILE:CG1 0.41 2.40 12 11:A:80:TYR:CE2 1:A:109:LEU:HB3 0.41 2.51 11 11:A:64:ASP:HB3 1:A:125:VAL:HG11 0.41 1.91 9 11:A:28:LEU:HG 1:A:149:ILE:CB 0.41 2.46 5 11:A:135:LYS:HG2 1:A:138:TYR:HB3 0.41 1.92 8 11:A:70:VAL:HG22 1:A:111:PHE:O 0.41 2.16 7 11:A:30:GLN:HG3 1:A:136:GLN:OE1 0.41 2.16 3 1
1:A:150:THR:HG22 1:A:150:THR:O 0.41 2.15 4 11:A:78:GLN:O 1:A:78:GLN:HG2 0.41 2.16 5 1
1:A:24:LEU:HD13 1:A:54:PHE:CD1 0.41 2.51 1 11:A:59:TYR:CE2 1:A:69:THR:CG2 0.41 3.03 2 11:A:67:LYS:HD2 1:A:125:VAL:HA 0.41 1.92 11 11:A:131:PHE:CB 1:A:143:ALA:O 0.41 2.69 11 1
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Atom-1 Atom-2 Clash(Å) Distance(Å) ModelsWorst Total
1:A:30:GLN:HE21 1:A:136:GLN:NE2 0.41 2.13 7 11:A:119:LYS:HD2 1:A:151:ASP:OD1 0.41 2.15 6 11:A:15:MET:HG3 1:A:16:ARG:CD 0.41 2.37 8 11:A:47:ASN:HB3 1:A:50:GLU:HG3 0.41 1.91 1 1
1:A:110:LEU:HD12 1:A:126:ALA:HB2 0.41 1.93 2 11:A:82:THR:HG22 1:A:91:LEU:H 0.41 1.76 2 11:A:30:GLN:HA 1:A:44:ALA:CA 0.41 2.45 11 11:A:133:ALA:HB3 1:A:141:CYS:O 0.41 2.16 7 11:A:53:LYS:O 1:A:74:ILE:HA 0.41 2.15 3 1
1:A:74:ILE:CD1 1:A:79:LEU:HB2 0.41 2.46 6 11:A:32:ILE:HG22 1:A:42:ALA:CB 0.41 2.45 10 21:A:32:ILE:HD11 1:A:54:PHE:CE1 0.41 2.50 8 11:A:15:MET:HG2 1:A:60:LYS:HG2 0.40 1.92 7 11:A:13:ASN:HB3 1:A:102:ILE:CG2 0.40 2.46 6 11:A:119:LYS:HB2 1:A:151:ASP:HB3 0.40 1.93 10 11:A:26:ASP:OD1 1:A:29:ASN:N 0.40 2.54 4 11:A:25:ASN:HB3 1:A:153:GLN:HG3 0.40 1.93 5 11:A:15:MET:SD 1:A:60:LYS:HD2 0.40 2.56 14 11:A:67:LYS:HE2 1:A:128:PRO:HG3 0.40 1.92 13 11:A:80:TYR:HB3 1:A:93:LYS:HE3 0.40 1.92 7 11:A:57:GLY:O 1:A:71:ILE:HG12 0.40 2.16 8 1
1:A:23:ILE:HD11 1:A:49:ASP:HA 0.40 1.92 3 11:A:16:ARG:NH1 1:A:18:ILE:HA 0.40 2.31 10 11:A:18:ILE:HG12 1:A:57:GLY:HA2 0.40 1.93 4 11:A:28:LEU:HB3 1:A:30:GLN:OE1 0.40 2.16 12 11:A:84:GLN:OE1 1:A:88:GLN:HB3 0.40 2.16 7 11:A:98:ILE:HD12 1:A:99:PRO:HD2 0.40 1.93 6 11:A:69:THR:CG2 1:A:110:LEU:HA 0.40 2.46 8 11:A:69:THR:HG21 1:A:110:LEU:CD2 0.40 2.47 8 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 143/151 (95%) 124±1 (86±1%) 16±1 (11±1%) 4±0 (3±0%) 10 46Continued on next page...
Page 29 Full wwPDB NMR Structure Validation Report 2KKI
Continued from previous page...Mol Chain Analysed Favoured Allowed Outliers Percentiles
All All 2002/2114 (95%) 1730 (86%) 221 (11%) 51 (3%) 10 46
All 5 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 104 GLY 141 A 64 ASP 141 A 18 ILE 141 A 97 GLU 71 A 84 GLN 2
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 127/133 (95%) 113±3 (89±3%) 14±3 (11±3%) 11 55
All All 1778/1862 (95%) 1582 (89%) 196 (11%) 11 55
All 71 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 16 ARG 131 A 131 PHE 121 A 45 LEU 101 A 152 PHE 91 A 82 THR 81 A 110 LEU 81 A 26 ASP 71 A 64 ASP 61 A 30 GLN 61 A 84 GLN 51 A 93 LYS 51 A 120 ASN 51 A 15 MET 51 A 102 ILE 4
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Continued from previous page...Mol Chain Res Type Models (Total)1 A 134 THR 41 A 114 GLU 41 A 13 ASN 41 A 29 ASN 31 A 59 TYR 31 A 139 TRP 31 A 80 TYR 31 A 136 GLN 31 A 47 ASN 31 A 74 ILE 31 A 108 ASN 21 A 155 LEU 21 A 55 ASP 21 A 75 SER 21 A 24 LEU 21 A 68 ILE 21 A 34 ARG 21 A 100 LYS 21 A 130 LEU 21 A 73 ARG 21 A 158 GLN 21 A 125 VAL 21 A 157 ASN 21 A 40 LEU 11 A 70 VAL 11 A 103 THR 11 A 128 PRO 11 A 31 SER 11 A 65 ASP 11 A 95 MET 11 A 98 ILE 11 A 156 GLU 11 A 78 GLN 11 A 88 GLN 11 A 28 LEU 11 A 69 THR 11 A 109 LEU 11 A 54 PHE 11 A 119 LYS 11 A 129 ASN 11 A 53 LYS 11 A 17 ILE 1
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Page 31 Full wwPDB NMR Structure Validation Report 2KKI
Continued from previous page...Mol Chain Res Type Models (Total)1 A 122 PHE 11 A 116 HIS 11 A 111 PHE 11 A 138 TYR 11 A 151 ASP 11 A 60 LYS 11 A 94 GLU 11 A 20 TYR 11 A 19 LYS 11 A 149 ILE 11 A 46 HIS 11 A 22 PHE 11 A 101 THR 11 A 25 ASN 11 A 67 LYS 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.
Page 32 Full wwPDB NMR Structure Validation Report 2KKI
7 Chemical shift validation i○
No chemical shift data were provided