i
Full wwPDB NMR Structure Validation Report ○
Feb 12, 2017 – 09:16 pm GMT
PDB ID : 2CT2
Title : Solution Structure of the RING domain of the Tripartite motif protein 32
Authors : Miyamoto, K.; Tochio, N.; Sato, M.; Koshiba, S.; Inoue, M.; Kigawa, T.;
Yokoyama, S.; RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposited on : 2005-05-23
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 at
http://wwpdb.org/validation/2016/NMRValidationReportHelp
i symbol.
with specific help available everywhere you see the ○
i were used in the production of this report:
The following versions of software and data (see references ○)
Cyrange
NmrClust
MolProbity
Percentile statistics
RCI
PANAV
ShiftChecker
Ideal geometry (proteins)
Ideal geometry (DNA, RNA)
Validation Pipeline (wwPDB-VP)
:
:
:
:
:
:
:
:
:
:
Kirchner and Güntert (2011)
Kelley et al. (1996)
4.02b-467
20161228.v01 (using entries in the PDB archive December 28th 2016)
v_1n_11_5_13_A (Berjanski et al., 2005)
Wang et al. (2010)
trunk28760
Engh & Huber (2001)
Parkinson et al. (1996)
recalc28949
Page 2
1
Full wwPDB NMR Structure Validation Report
2CT2
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Overall quality at a glance ○
The following experimental techniques were used to determine the structure:
SOLUTION NMR
The overall completeness of chemical shifts assignment is 91%.
Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in
the following graphic. The table shows the number of entries on which the scores are based.
Metric
Clashscore
Ramachandran outliers
Sidechain outliers
Whole archive
(#Entries)
125131
121729
121581
NMR archive
(#Entries)
11601
10391
10367
The table below summarises the geometric issues observed across the polymeric chains and their
fit to the experimental data. The red, orange, yellow and green segments indicate the fraction
of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. A cyan
segment indicates the fraction of residues that are not part of the well-defined cores, and a grey segment represents the fraction of residues that are not modelled. The numeric value for each fraction
is indicated below the corresponding segment, with a dot representing fractions <=5%
Mol
Chain
Length
1
A
88
Quality of chain
Page 3
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Full wwPDB NMR Structure Validation Report
2CT2
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Ensemble composition and analysis ○
This entry contains 20 models. Model 6 is the overall representative, medoid model (most similar
to other models). The authors have identified model 1 as representative, based on the following
criterion: lowest energy.
The following residues are included in the computation of the global validation metrics.
Well-defined core
1
Well-defined (core) protein residues
Residue range (total)
Backbone RMSD (Å)
A:15-A:51, A:56-A:81 (63)
0.18
Medoid model
6
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 1 single-model cluster was found.
Cluster number
1
2
Single-model clusters
Models
1, 2, 3, 4, 6, 7, 8, 10, 11, 12, 14, 15, 16, 18, 19, 20
5, 13, 17
9
Page 4
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Full wwPDB NMR Structure Validation Report
2CT2
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Entry composition ○
There are 2 unique types of molecules in this entry. The entry contains 1323 atoms, of which 665
are hydrogens and 0 are deuteriums.
• Molecule 1 is a protein called Tripartite motif protein 32.
Mol
Chain
Residues
1
A
88
Atoms
Total C
H
N
1321 402 665 117
O
129
S
8
Trace
0
There are 13 discrepancies between the modelled and reference sequences:
Chain
A
A
A
A
A
A
A
A
A
A
A
A
A
Residue
1
2
3
4
5
6
7
83
84
85
86
87
88
Modelled
GLY
SER
SER
GLY
SER
SER
GLY
SER
GLY
PRO
SER
SER
GLY
Actual
-
Comment
CLONING ARTIFACT
CLONING ARTIFACT
CLONING ARTIFACT
CLONING ARTIFACT
CLONING ARTIFACT
CLONING ARTIFACT
CLONING ARTIFACT
CLONING ARTIFACT
CLONING ARTIFACT
CLONING ARTIFACT
CLONING ARTIFACT
CLONING ARTIFACT
CLONING ARTIFACT
• Molecule 2 is ZINC ION (three-letter code: ZN) (formula: Zn).
Mol
Chain
Residues
2
A
2
Atoms
Total Zn
2
2
Reference
UNP Q13049
UNP Q13049
UNP Q13049
UNP Q13049
UNP Q13049
UNP Q13049
UNP Q13049
UNP Q13049
UNP Q13049
UNP Q13049
UNP Q13049
UNP Q13049
UNP Q13049
Page 5
4
4.1
Full wwPDB NMR Structure Validation Report
2CT2
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Residue-property plots ○
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 the
same as shown in the summary in section 1 of this report. The second graphic shows the sequence
where residues are colour-coded according to the number of geometric quality criteria for which
they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretches
of 2 or more consecutive residues without any outliers are shown as green connectors. Residues
which are classified as ill-defined in the NMR ensemble, are shown in cyan with an underline
colour-coded according to the previous scheme. Residues which were present in the experimental
sample, but not modelled in the final structure are shown in grey.
• Molecule 1: Tripartite motif protein 32
L71
C59
P60
F61
C62
S63
K64
I65
T66
R67
I68
S52
S53
I54
N55
L46
E47
K48
R43
L30
R31
P32
K33
L34
L35
H36
C37
G38
H39
T40
S24
F25
T26
E27
P19
L74
T75
D76
N77
L78
T79
V80
L81
K82
S83
G84
P85
S86
S87
G88
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
V15
L16
Chain A:
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: Tripartite motif protein 32
4.2.2
Score per residue for model 2
• Molecule 1: Tripartite motif protein 32
Chain A:
N77
L78
T79
V80
L71
T72
Q73
L74
T66
R67
I68
L50
A51
S52
S53
I54
N55
L46
E47
R43
P32
K33
L34
L35
H36
C37
G38
H39
T40
S24
F25
T26
E27
E28
Q29
L81
K82
S83
G84
P85
S86
S87
G88
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
V15
L16
E17
Chain A:
L71
T72
Q73
L74
T75
D76
N77
L78
T79
V80
L81
K82
S83
G84
P85
S86
S87
G88
4.2.6
Chain A:
• Molecule 1: Tripartite motif protein 32
Score per residue for model 6 (medoid)
T66
R67
I68
C59
P60
F61
C62
S63
R43
Q44
C45
L46
E47
K48
L49
L50
A51
S52
S53
I54
N55
Q29
L30
R31
P32
K33
L34
L35
H36
C37
G38
H39
T40
4.2.5
L78
T79
V80
L81
K82
S83
G84
P85
S86
S87
G88
L74
L71
T66
R67
I68
S63
C59
S52
S53
I54
N55
L46
E47
P32
K33
L34
L35
H36
C37
G38
4.2.4
S24
F25
T26
E27
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
N77
L78
T79
V80
L81
K82
S83
G84
P85
S86
S87
G88
Score per residue for model 4
• Molecule 1: Tripartite motif protein 32
Chain A:
Score per residue for model 5
• Molecule 1: Tripartite motif protein 32
Chain A:
L74
L71
T66
R67
I68
S63
S52
S53
I54
N55
G56
V57
R58
C59
P32
K33
L34
L35
H36
C37
G38
H39
T40
I41
C42
R43
Q44
C45
L46
E47
K48
L49
S24
F25
T26
P19
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
V15
L16
4.2.3
F25
T26
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
V15
L16
E17
C18
P19
K82
S83
G84
P85
S86
S87
G88
L74
T75
D76
N77
L78
T79
T66
R67
I68
C59
P60
F61
C62
S63
L46
E47
K48
L49
L50
A51
S52
S53
I54
N55
R43
L34
L35
H36
C37
G38
H39
T40
M22
E23
S24
F25
T26
E27
E28
Q29
L30
R31
C18
P19
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
Page 6
Full wwPDB NMR Structure Validation Report
2CT2
Score per residue for model 3
• Molecule 1: Tripartite motif protein 32
Chain A:
V80
L81
K82
S83
G84
P85
S86
S87
G88
4.2.10
• Molecule 1: Tripartite motif protein 32
Score per residue for model 10
K64
I65
T66
R67
I68
T69
S70
L71
T72
Q73
L74
T75
D76
N77
L78
T79
F61
S52
S53
I54
N55
C45
L46
E47
K48
4.2.9
K82
S83
G84
P85
S86
S87
G88
L46
E47
K48
R43
P32
K33
L34
L35
H36
C37
G38
H39
T40
F25
P19
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
K64
I65
T66
R67
I68
T69
S70
L71
T72
Q73
L74
T75
D76
N77
L78
L46
E47
K64
I65
T66
R67
I68
T69
S70
L71
T72
Q73
L74
T75
D76
N77
L78
T79
V80
L81
F61
Chain A:
S52
S53
I54
N55
• Molecule 1: Tripartite motif protein 32
S52
S53
I54
N55
Score per residue for model 8
R43
L30
R31
P32
K33
L34
L35
H36
C37
G38
H39
T40
E23
S24
F25
T26
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
V15
L16
E17
4.2.8
G38
T79
V80
L81
K82
S83
G84
P85
S86
S87
G88
4.2.7
L34
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
V15
L16
E17
C18
P19
I20
C21
M22
E23
S24
F25
T26
E27
L78
T79
V80
L81
K82
S83
G84
P85
S86
S87
G88
R67
I68
T69
S70
L71
T72
Q73
L74
C59
P60
F61
C62
S63
K64
I65
T66
R43
Q44
C45
L46
E47
K48
L49
L50
A51
S52
S53
I54
N55
L30
R31
P32
K33
L34
L35
H36
C37
G38
H39
T40
E23
S24
F25
T26
E27
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
V15
L16
E17
C18
P19
Page 7
Full wwPDB NMR Structure Validation Report
Score per residue for model 7
• Molecule 1: Tripartite motif protein 32
Chain A:
Score per residue for model 9
• Molecule 1: Tripartite motif protein 32
Chain A:
2CT2
T75
D76
N77
L78
T79
V80
L81
K82
S83
G84
P85
S86
S87
G88
L74
L71
C59
P60
F61
C62
S63
K64
I65
T66
R67
I68
S52
S53
I54
N55
4.2.13
T66
R67
I68
T69
S70
L71
T72
Q73
L74
C59
P60
F61
C62
S63
S52
S53
I54
N55
G56
L46
E47
K48
P32
K33
L34
L35
H36
C37
G38
H39
T40
I41
E23
S24
F25
T26
E27
E28
P19
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
4.2.12
Q29
L30
R31
P32
K33
L34
L35
H36
C37
G38
H39
T40
I41
C42
R43
Q44
C45
L46
N77
L78
T79
V80
L81
K82
S83
G84
P85
S86
S87
G88
L78
T79
V80
L81
K82
S83
G84
P85
S86
S87
G88
L74
T75
S70
L71
C62
S63
K64
I65
T66
R67
Q44
C45
L46
E47
K48
L49
L50
A51
S52
S53
I54
N55
G56
V57
R58
C59
E28
Q29
L30
R31
P32
K33
L34
L35
H36
C37
G38
H39
T40
F25
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
V15
L16
E17
4.2.11
F25
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
V15
L16
E17
C18
P19
L78
T79
V80
L81
K82
S83
G84
P85
S86
S87
G88
Q73
L74
T75
D76
N77
F61
C62
S63
K64
I65
T66
R67
I68
T69
S52
S53
I54
N55
P32
K33
L34
L35
H36
C37
G38
H39
T40
I41
C42
R43
Q44
C45
L46
M22
E23
S24
F25
T26
E27
C18
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
Page 8
Full wwPDB NMR Structure Validation Report
2CT2
Chain A:
Score per residue for model 11
• Molecule 1: Tripartite motif protein 32
Chain A:
Score per residue for model 12
• Molecule 1: Tripartite motif protein 32
Chain A:
Score per residue for model 13
• Molecule 1: Tripartite motif protein 32
Chain A:
C59
P60
F61
C62
S63
K64
I65
4.2.17
L78
T79
V80
L81
K82
S83
G84
P85
S86
S87
L74
T75
L71
T66
R67
I68
S52
S53
I54
N55
G56
C45
L46
E47
I41
L34
L35
H36
C37
G38
F25
T26
E27
M22
C18
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
4.2.16
L50
A51
S52
S53
I54
N55
G88
K82
S83
G84
P85
S86
S87
G88
R67
I68
T69
S70
L71
T72
Q73
L74
T75
D76
N77
L78
T79
V80
L81
C62
S52
S53
I54
N55
R43
Q44
C45
L46
E47
K48
L30
R31
P32
K33
L34
L35
H36
C37
G38
E23
S24
F25
T26
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
V15
4.2.15
E23
S24
F25
T26
E27
E28
Q29
L30
R31
P32
K33
L34
L35
H36
C37
G38
H39
T40
I41
C42
R43
Q44
C45
L46
E47
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
V15
L16
E17
C18
P19
S83
G84
P85
S86
S87
G88
L74
T75
D76
N77
L78
T79
V80
L81
K82
L71
T66
R67
I68
S52
S53
I54
N55
L30
R31
P32
K33
L34
L35
H36
C37
G38
H39
T40
I41
C42
R43
Q44
C45
L46
T26
E27
P19
I20
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
V15
4.2.14
N77
L78
T79
V80
L81
K82
S83
G84
P85
S86
S87
G88
L74
L71
T66
R67
I68
Page 9
Full wwPDB NMR Structure Validation Report
Score per residue for model 14
• Molecule 1: Tripartite motif protein 32
Chain A:
Score per residue for model 15
• Molecule 1: Tripartite motif protein 32
Chain A:
Score per residue for model 16
• Molecule 1: Tripartite motif protein 32
Chain A:
Score per residue for model 17
• Molecule 1: Tripartite motif protein 32
Chain A:
2CT2
N77
L78
T79
V80
L81
K82
S83
G84
P85
S86
S87
G88
L74
L71
K64
I65
T66
R67
I68
F61
L46
E47
K48
L49
L50
A51
S52
S53
I54
N55
G56
V57
R43
4.2.20
L74
T75
D76
L71
T66
R67
I68
S63
C59
L50
A51
S52
S53
I54
N55
L34
L35
H36
C37
G38
H39
T40
I41
C42
R43
Q44
C45
L46
E47
L30
E23
S24
F25
P19
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
V15
L16
4.2.19
L30
R31
P32
K33
L34
L35
H36
C37
G38
H39
T40
N77
L78
T79
V80
L81
K82
S83
G84
P85
S86
S87
G88
N77
L78
T79
V80
L81
K82
S83
G84
P85
S86
S87
G88
L74
C59
P60
F61
C62
S63
K64
I65
T66
R67
I68
T69
S70
S52
S53
I54
N55
G56
L34
L35
H36
C37
G38
H39
T40
I41
C42
R43
Q44
C45
L46
E47
K48
L30
F25
T26
C18
P19
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
4.2.18
E23
S24
F25
G1
S2
S3
G4
S5
S6
G7
N8
L9
D10
A11
L12
R13
E14
V15
L16
E17
C18
P19
Page 10
Full wwPDB NMR Structure Validation Report
2CT2
Score per residue for model 18
• Molecule 1: Tripartite motif protein 32
Chain A:
Score per residue for model 19
• Molecule 1: Tripartite motif protein 32
Chain A:
Score per residue for model 20
• Molecule 1: Tripartite motif protein 32
Chain A:
Page 11
5
Full wwPDB NMR Structure Validation Report
2CT2
i
Refinement protocol and experimental data overview ○
The models were refined using the following method: torsion angle dynamics.
Of the 100 calculated structures, 20 were deposited, based on the following criterion: target function, structures with the least restraint violations.
The following table shows the software used for structure solution, optimisation and refinement.
Software name
CYANA
CYANA
Classification
structure solution
refinement
Version
2.0.17
2.0.17
The following table shows chemical shift validation statistics as aggregates over all chemical shift
files. Detailed validation can be found in section 7 of this report.
Chemical shift file(s)
Number of chemical shift lists
Total number of shifts
Number of shifts mapped to atoms
Number of unparsed shifts
Number of shifts with mapping errors
Number of shifts with mapping warnings
Assignment completeness (well-defined parts)
BMRB entry 11317
1
1007
1007
0
0
0
91%
No validations of the models with respect to experimental NMR restraints is performed at this
time.
Page 12
6
Full wwPDB NMR Structure Validation Report
2CT2
i
Model quality ○
6.1
i
Standard geometry ○
Bond lengths and bond angles in the following residue types are not validated in this section:
ZN
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
i
Too-close contacts ○
In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms
and hydrogen atoms in each chain respectively. The H(added) column lists the number of hydrogen
atoms added and optimized by MolProbity. The Clashes column lists the number of clashes
averaged over the ensemble.
Mol
1
All
Chain
A
All
Non-H
493
9900
H(model)
512
10240
H(added)
512
10240
Clashes
27±4
532
The all-atom clashscore is defined as the number of clashes found per 1000 atoms (including
hydrogen atoms). The all-atom clashscore for this structure is 26.
All unique clashes are listed below, sorted by their clash magnitude.
Atom-1
Atom-2
Clash(Å)
1:A:68:ILE:CD1
1:A:47:GLU:OE2
1:A:68:ILE:HD13
1:A:68:ILE:HD13
1:A:34:LEU:HD11
1:A:36:HIS:CD2
1:A:32:PRO:HB3
1:A:35:LEU:HD21
1:A:35:LEU:HD22
1:A:34:LEU:HD13
1:A:24:SER:O
1:A:27:GLU:OE2
1:A:74:LEU:HD23
1:A:71:LEU:HD11
1:A:74:LEU:HD23
1:A:74:LEU:HB3
1:A:38:GLY:O
1:A:66:THR:HG23
1:A:80:VAL:HG21
1:A:46:LEU:HD11
1:A:66:THR:OG1
1:A:77:ASN:OD1
1:A:26:THR:HG23
1:A:81:LEU:HD13
0.93
0.85
0.81
0.79
0.79
0.77
0.73
0.71
0.70
0.70
0.69
0.68
Models
Worst Total
1.94
18
12
1.71
9
5
1.53
18
9
1.54
10
9
1.78
3
20
2.15
8
15
1.59
13
12
1.62
10
4
1.87
14
5
1.86
1
3
1.86
3
6
1.88
14
2
Continued on next page...
Distance(Å)
Page 13
Full wwPDB NMR Structure Validation Report
Continued from previous page...
Atom-1
Atom-2
Clash(Å)
1:A:46:LEU:HD23
1:A:34:LEU:HD22
1:A:68:ILE:O
1:A:35:LEU:HD21
1:A:36:HIS:CD2
1:A:68:ILE:HD11
1:A:25:PHE:CD2
1:A:40:THR:HG21
1:A:47:GLU:OE1
1:A:46:LEU:HD21
1:A:27:GLU:CD
1:A:77:ASN:OD1
1:A:36:HIS:CG
1:A:32:PRO:CB
1:A:27:GLU:CD
1:A:47:GLU:CD
1:A:26:THR:O
1:A:36:HIS:CE1
1:A:71:LEU:O
1:A:23:GLU:HB3
1:A:30:LEU:CD2
1:A:68:ILE:HD13
1:A:74:LEU:C
1:A:30:LEU:HD21
1:A:78:LEU:H
1:A:78:LEU:HD13
1:A:68:ILE:HD13
1:A:46:LEU:HD23
1:A:15:VAL:O
1:A:49:LEU:HD13
1:A:78:LEU:CD2
1:A:78:LEU:HA
1:A:78:LEU:C
1:A:68:ILE:HD13
1:A:50:LEU:HD13
1:A:41:ILE:HD11
1:A:71:LEU:O
1:A:46:LEU:CD2
1:A:19:PRO:CD
1:A:40:THR:HG21
1:A:37:CYS:CB
1:A:71:LEU:HD22
1:A:77:ASN:OD1
1:A:68:ILE:HD12
1:A:46:LEU:CD1
1:A:66:THR:CG2
1:A:74:LEU:HD23
1:A:80:VAL:HG21
1:A:77:ASN:ND2
1:A:71:LEU:HD21
1:A:74:LEU:HD21
1:A:81:LEU:HD13
1:A:80:VAL:HG13
1:A:66:THR:HG23
1:A:80:VAL:HG21
1:A:81:LEU:HD22
1:A:71:LEU:HD11
1:A:81:LEU:HD21
1:A:66:THR:O
1:A:74:LEU:HD11
1:A:30:LEU:HD13
1:A:44:GLN:NE2
1:A:74:LEU:CB
1:A:74:LEU:HD12
1:A:44:GLN:NE2
1:A:78:LEU:HD13
1:A:78:LEU:H
1:A:74:LEU:CD2
1:A:71:LEU:CD2
1:A:15:VAL:HG23
1:A:58:ARG:O
1:A:78:LEU:C
1:A:81:LEU:HD12
1:A:78:LEU:CD2
1:A:74:LEU:CG
1:A:71:LEU:HD23
1:A:61:PHE:CE2
1:A:74:LEU:CD1
1:A:74:LEU:HD21
1:A:40:THR:O
1:A:77:ASN:CG
1:A:62:CYS:SG
0.68
0.68
0.68
0.66
0.66
0.65
0.65
0.64
0.63
0.62
0.62
0.62
0.62
0.61
0.61
0.60
0.60
0.59
0.59
0.58
0.57
0.56
0.55
0.55
0.55
0.55
0.55
0.55
0.55
0.54
0.53
0.53
0.53
0.52
0.52
0.52
0.52
0.51
0.51
0.51
0.51
Models
Worst Total
1.64
15
10
1.89
17
6
1.89
15
1
2.20
15
14
2.78
8
11
1.68
19
8
2.27
15
11
2.08
2
2
1.92
4
8
1.71
8
7
2.12
12
1
1.95
8
4
2.30
8
2
2.26
13
6
2.16
14
1
2.16
9
6
1.97
5
1
2.56
18
4
1.98
9
2
1.76
19
1
2.68
5
7
2.29
6
7
2.22
10
6
2.16
11
4
1.62
9
8
1.61
8
12
2.29
18
4
2.31
7
4
1.99
14
1
2.03
11
2
2.77
16
7
1.80
10
1
2.76
4
13
2.34
16
6
1.80
6
3
2.39
12
1
2.58
9
2
2.35
8
7
2.59
7
8
2.25
19
3
2.99
2
5
Continued on next page...
Distance(Å)
2CT2
Page 14
Full wwPDB NMR Structure Validation Report
Continued from previous page...
Atom-1
Atom-2
Clash(Å)
1:A:25:PHE:CD2
1:A:43:ARG:HG3
1:A:64:LYS:O
1:A:40:THR:CG2
1:A:29:GLN:O
1:A:78:LEU:HD22
1:A:69:THR:HG22
1:A:19:PRO:HB2
1:A:66:THR:O
1:A:74:LEU:C
1:A:18:CYS:SG
1:A:32:PRO:CB
1:A:59:CYS:O
1:A:70:SER:HB3
1:A:16:LEU:O
1:A:69:THR:HG22
1:A:69:THR:N
1:A:15:VAL:O
1:A:40:THR:HG21
1:A:74:LEU:O
1:A:34:LEU:N
1:A:34:LEU:HD13
1:A:50:LEU:O
1:A:28:GLU:O
1:A:27:GLU:HG3
1:A:70:SER:OG
1:A:49:LEU:HB3
1:A:40:THR:OG1
1:A:23:GLU:O
1:A:68:ILE:HG22
1:A:35:LEU:HD21
1:A:68:ILE:HD12
1:A:78:LEU:CD2
1:A:74:LEU:HD12
1:A:50:LEU:HA
1:A:23:GLU:HB3
1:A:33:LYS:NZ
1:A:68:ILE:HG21
1:A:78:LEU:HD22
1:A:25:PHE:O
1:A:77:ASN:ND2
1:A:80:VAL:HG11
1:A:44:GLN:N
1:A:65:ILE:C
1:A:77:ASN:ND2
1:A:30:LEU:C
1:A:79:THR:N
1:A:73:GLN:OE1
1:A:61:PHE:CZ
1:A:68:ILE:N
1:A:74:LEU:CD1
1:A:41:ILE:HG23
1:A:80:VAL:CG2
1:A:63:SER:N
1:A:72:THR:HG22
1:A:25:PHE:CD2
1:A:73:GLN:NE2
1:A:73:GLN:OE1
1:A:17:GLU:N
1:A:77:ASN:OD1
1:A:74:LEU:HD12
1:A:75:THR:O
1:A:40:THR:OG1
1:A:51:ALA:C
1:A:29:GLN:C
1:A:81:LEU:HD22
1:A:72:THR:HG22
1:A:57:VAL:HG13
1:A:77:ASN:ND2
1:A:24:SER:C
1:A:73:GLN:HB3
1:A:46:LEU:HD13
1:A:70:SER:O
1:A:79:THR:N
1:A:74:LEU:C
1:A:57:VAL:HG22
1:A:30:LEU:CD1
1:A:71:LEU:O
1:A:74:LEU:CA
1:A:78:LEU:N
1:A:81:LEU:HD23
1:A:79:THR:HG22
0.50
0.50
0.50
0.50
0.50
0.50
0.50
0.49
0.49
0.49
0.49
0.49
0.48
0.48
0.48
0.48
0.47
0.47
0.47
0.47
0.47
0.47
0.46
0.46
0.46
0.46
0.46
0.45
0.45
0.45
0.45
0.45
0.45
0.45
0.45
0.44
0.44
0.44
0.44
0.44
0.44
Models
Worst Total
2.41
10
4
2.21
18
5
2.50
11
10
2.73
2
1
2.50
5
3
2.21
20
4
2.06
10
1
2.42
13
10
2.45
20
5
2.80
10
3
2.47
18
1
2.91
13
1
2.46
6
7
1.85
15
1
2.67
8
5
2.23
6
1
2.47
7
1
2.48
5
8
2.08
8
3
2.10
13
1
2.48
5
9
2.10
20
8
2.54
20
4
2.52
11
1
1.86
16
1
2.11
12
1
1.88
20
1
2.50
8
1
2.54
20
7
1.89
5
2
1.88
3
1
2.12
18
1
2.79
10
2
2.31
14
4
1.88
11
1
2.42
2
2
2.50
4
1
2.43
18
3
2.27
2
4
2.13
7
1
2.28
9
2
Continued on next page...
Distance(Å)
2CT2
Page 15
Full wwPDB NMR Structure Validation Report
Continued from previous page...
Atom-1
Atom-2
Clash(Å)
1:A:41:ILE:CG2
1:A:70:SER:HB3
1:A:59:CYS:O
1:A:24:SER:O
1:A:41:ILE:HG22
1:A:24:SER:O
1:A:40:THR:CG2
1:A:27:GLU:O
1:A:79:THR:HG23
1:A:15:VAL:C
1:A:72:THR:O
1:A:33:LYS:CE
1:A:66:THR:O
1:A:77:ASN:O
1:A:25:PHE:CG
1:A:26:THR:O
1:A:32:PRO:HG3
1:A:46:LEU:HD21
1:A:26:THR:C
1:A:74:LEU:CD1
1:A:39:HIS:CE1
1:A:27:GLU:CD
1:A:34:LEU:O
1:A:73:GLN:O
1:A:18:CYS:O
1:A:18:CYS:O
1:A:35:LEU:HD12
1:A:19:PRO:HG2
1:A:15:VAL:O
1:A:70:SER:C
1:A:78:LEU:N
1:A:26:THR:O
1:A:26:THR:O
1:A:34:LEU:CD1
1:A:20:ILE:HD12
1:A:27:GLU:OE2
1:A:29:GLN:NE2
1:A:42:CYS:O
1:A:15:VAL:O
1:A:26:THR:O
1:A:20:ILE:HD12
1:A:45:CYS:HB2
1:A:73:GLN:CG
1:A:63:SER:HA
1:A:25:PHE:C
1:A:45:CYS:HB2
1:A:26:THR:CG2
1:A:77:ASN:CG
1:A:28:GLU:C
1:A:80:VAL:N
1:A:17:GLU:N
1:A:73:GLN:C
1:A:71:LEU:O
1:A:68:ILE:CG1
1:A:80:VAL:HG22
1:A:32:PRO:HB3
1:A:27:GLU:C
1:A:80:VAL:CG2
1:A:74:LEU:CD2
1:A:28:GLU:N
1:A:74:LEU:C
1:A:61:PHE:HB3
1:A:27:GLU:O
1:A:75:THR:O
1:A:74:LEU:O
1:A:22:MET:HA
1:A:22:MET:SD
1:A:59:CYS:SG
1:A:61:PHE:CE2
1:A:15:VAL:CG2
1:A:72:THR:N
1:A:78:LEU:HD22
1:A:28:GLU:N
1:A:30:LEU:O
1:A:38:GLY:O
1:A:45:CYS:HB3
1:A:81:LEU:HD22
1:A:29:GLN:C
1:A:43:ARG:C
1:A:16:LEU:C
1:A:30:LEU:C
1:A:41:ILE:CG2
0.43
0.43
0.43
0.43
0.43
0.43
0.43
0.43
0.43
0.42
0.42
0.42
0.42
0.42
0.42
0.42
0.42
0.42
0.42
0.42
0.41
0.41
0.41
0.41
0.41
0.41
0.41
0.41
0.41
0.41
0.41
0.41
0.40
0.40
0.40
0.40
0.40
0.40
0.40
0.40
0.40
Models
Worst Total
2.42
17
5
2.44
9
1
2.14
2
8
2.57
9
1
1.89
10
3
2.67
9
1
2.87
18
2
2.56
1
1
2.28
10
1
2.72
8
8
2.56
8
1
2.67
4
1
2.67
7
2
2.14
13
2
2.50
7
5
2.58
4
2
2.44
17
5
2.45
19
1
2.73
2
1
2.88
15
1
2.51
10
1
2.59
10
1
2.39
8
5
2.39
8
2
2.16
10
1
2.79
9
3
2.55
12
1
2.51
12
1
2.69
14
1
2.74
8
1
2.30
3
1
2.54
2
1
2.39
18
1
2.62
3
1
1.92
9
1
2.16
17
1
2.75
1
1
2.59
3
1
2.60
1
1
2.59
8
1
2.47
14
1
Continued on next page...
Distance(Å)
2CT2
Page 16
Full wwPDB NMR Structure Validation Report
2CT2
Continued from previous page...
Atom-1
Atom-2
Clash(Å)
Distance(Å)
1:A:59:CYS:O
1:A:63:SER:CA
0.40
2.69
6.3
6.3.1
Models
Worst Total
6
1
i
Torsion angles ○
i
Protein backbone ○
In the following table, the Percentiles column shows the percent Ramachandran outliers of the chain
as a percentile score with respect to all PDB entries followed by that with respect to all NMR
entries. The Analysed column shows the number of residues for which the backbone conformation
was analysed and the total number of residues.
Mol
Chain
Analysed
Favoured
Allowed
Outliers
Percentiles
1
A
63/88 (72%)
48±2 (77±3%)
12±2 (19±3%)
3±1 (4±2%)
5
30
All
All
1260/1760 (72%)
968 (77%)
237 (19%)
55 (4%)
5
30
All 9 unique Ramachandran outliers are listed below. They are sorted by the frequency of occurrence in the ensemble.
Mol
1
1
1
1
1
1
1
1
1
6.3.2
Chain
A
A
A
A
A
A
A
A
A
Res
74
67
65
16
24
25
30
27
15
Type
LEU
ARG
ILE
LEU
SER
PHE
LEU
GLU
VAL
Models (Total)
20
8
8
8
3
3
3
1
1
i
Protein sidechains ○
In the following table, the Percentiles column shows the percent sidechain outliers of the chain
as a percentile score with respect to all PDB entries followed by that with respect to all NMR
entries. The Analysed column shows the number of residues for which the sidechain conformation
was analysed and the total number of residues.
Mol
Chain
Analysed
Rotameric
Outliers
Percentiles
1
A
60/79 (76%)
56±2 (94±3%)
4±2 (6±3%)
26
72
All
All
1200/1580 (76%)
1126 (94%)
74 (6%)
26
72
Page 17
Full wwPDB NMR Structure Validation Report
2CT2
All 18 unique residues with a non-rotameric sidechain are listed below. They are sorted by the
frequency of occurrence in the ensemble.
Mol
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
6.3.3
Chain
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
Res
78
48
43
74
67
68
26
27
29
76
73
31
70
33
24
66
28
69
Type
LEU
LYS
ARG
LEU
ARG
ILE
THR
GLU
GLN
ASP
GLN
ARG
SER
LYS
SER
THR
GLU
THR
Models (Total)
20
11
11
6
4
3
2
2
2
2
2
2
2
1
1
1
1
1
i
RNA ○
There are no RNA molecules in this entry.
6.4
i
Non-standard residues in protein, DNA, RNA chains ○
There are no non-standard protein/DNA/RNA residues in this entry.
6.5
i
Carbohydrates ○
There are no carbohydrates in this entry.
6.6
i
Ligand geometry ○
Of 2 ligands modelled in this entry, 2 are monoatomic - leaving 0 for Mogul analysis.
6.7
i
Other polymers ○
There are no such molecules in this entry.
Page 18
6.8
Full wwPDB NMR Structure Validation Report
i
Polymer linkage issues ○
There are no chain breaks in this entry.
2CT2
Page 19
7
Full wwPDB NMR Structure Validation Report
2CT2
i
Chemical shift validation ○
The completeness of assignment taking into account all chemical shift lists is 91% for the welldefined parts and 86% for the entire structure.
7.1
Chemical shift list 1
File name: BMRB entry 11317
Chemical shift list name: assigned_chem_shift_list_1
7.1.1
i
Bookkeeping ○
The following table shows the results of parsing the chemical shift list and reports the number of
nuclei with statistically unusual chemical shifts.
Total number of shifts
Number of shifts mapped to atoms
Number of unparsed shifts
Number of shifts with mapping errors
Number of shifts with mapping warnings
Number of shift outliers (ShiftChecker)
7.1.2
1007
1007
0
0
0
0
i
Chemical shift referencing ○
The following table shows the suggested chemical shift referencing corrections.
Nucleus
13
Cα
13
Cβ
13 0
C
15
N
7.1.3
# values
80
76
74
75
Correction ± precision, ppm
-0.46 ± 0.14
0.20 ± 0.11
-0.31 ± 0.20
0.50 ± 0.37
Suggested action
None needed (< 0.5 ppm)
None needed (< 0.5 ppm)
None needed (< 0.5 ppm)
None needed (< 0.5 ppm)
i
Completeness of resonance assignments ○
The following table shows the completeness of the chemical shift assignments for the well-defined
regions of the structure. The overall completeness is 91%, i.e. 714 atoms were assigned a chemical
shift out of a possible 788. 0 out of 14 assigned methyl groups (LEU and VAL) were assigned
stereospecifically.
Backbone
Sidechain
Total
304/309 (98%)
384/447 (86%)
H
123/123 (100%)
235/262 (90%)
1
15
C
N
121/126 (96%) 60/60 (100%)
145/166 (87%)
4/19 (21%)
Continued on next page...
13
Page 20
Full wwPDB NMR Structure Validation Report
Continued from previous page...
1
H
Total
Aromatic
26/32 (81%)
14/18 (78%)
Overall
714/788 (91%) 372/403 (92%)
C
12/12 (100%)
278/304 (91%)
13
2CT2
N
0/2 (0%)
64/81 (79%)
15
The following table shows the completeness of the chemical shift assignments for the full structure.
The overall completeness is 86%, i.e. 883 atoms were assigned a chemical shift out of a possible
1032. 1 out of 16 assigned methyl groups (LEU and VAL) were assigned stereospecifically.
Backbone
Sidechain
Aromatic
Overall
7.1.4
Total
383/432 (89%)
474/568 (83%)
26/32 (81%)
883/1032 (86%)
H
154/172 (90%)
291/335 (87%)
14/18 (78%)
459/525 (87%)
1
C
154/176 (88%)
177/208 (85%)
12/12 (100%)
343/396 (87%)
13
N
75/84 (89%)
6/25 (24%)
0/2 (0%)
81/111 (73%)
15
i
Statistically unusual chemical shifts ○
There are no statistically unusual chemical shifts.
7.1.5
i
Random Coil Index (RCI) plots ○
The image below reports random coil index values for the protein chains in the structure. The
height of each bar gives a probability of a given residue to be disordered, as predicted from
the available chemical shifts and the amino acid sequence. A value above 0.2 is an indication
of significant predicted disorder. The colour of the bar shows whether the residue is in the welldefined core (black) or in the ill-defined residue ranges (cyan), as described in section 2 on ensemble
composition.
Random coil index (RCI) for chain A: