full wwpdb nmr structure validation report o...

Full wwPDB NMR Structure Validation Report iO

May 28, 2020 � 10:45 pm BST

PDB ID : 2KVOTitle : Solution NMR structure of Photosystem II reaction center Psb28 protein from

Synechocystis sp.(strain PCC 6803), Northeast Structural Genomics Consor-tium Target SgR171

Authors : Yang, Y.; Ramelot, T.A.; Cort, J.R.; Wang, D.; Ciccosanti, C.; Hamilton, K.;Nair, R.; Rost, B.; Acton, T.B.; Xiao, R.; Everett, J.K.; Montelione, G.T.;Kennedy, M.A.; Northeast Structural Genomics Consortium (NESG)

Deposited on : 2010-03-22

This is a Full wwPDB NMR Structure Validation Report for a publicly released PDB entry.

We welcome your comments at [email protected]

A user guide is available athttps://www.wwpdb.org/validation/2017/NMRValidationReportHelp

with speci�c help available everywhere you see the iO symbol.

The following versions of software and data (see references iO) were used in the production of this report:

Cyrange : Kirchner and Güntert (2011)NmrClust : Kelley et al. (1996)

MolProbity : 4.02b-467Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)

RCI : v_1n_11_5_13_A (Berjanski et al., 2005)PANAV : Wang et al. (2010)

ShiftChecker : 2.11Ideal geometry (proteins) : Engh & Huber (2001)

Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : 2.11

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



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

Full wwPDB NMR Structure Validation Report 2KVO

1 Overall quality at a glance iO

The following experimental techniques were used to determine the structure:SOLUTION NMR

The overall completeness of chemical shifts assignment was not calculated.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.

MetricWhole archive(#Entries)

NMR archive(#Entries)

Clashscore 158937 12864Ramachandran outliers 154571 11451

Sidechain outliers 154315 11428

The table below summarises the geometric issues observed across the polymeric chains and their�t to the experimental data. The red, orange, yellow and green segments indicate the fractionof residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. A cyansegment indicates the fraction of residues that are not part of the well-de�ned cores, and a grey seg-ment represents the fraction of residues that are not modelled. The numeric value for each fractionis indicated below the corresponding segment, with a dot representing fractions <=5%

Mol Chain Length Quality of chain

1 A 120

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


2 Ensemble composition and analysis iO

This entry contains 20 models. Model 18 is the overall representative, medoid model (most similarto other models). The authors have identi�ed model 1 as representative, based on the followingcriterion: lowest energy.

The following residues are included in the computation of the global validation metrics.

Well-de�ned (core) protein residuesWell-de�ned core Residue range (total) Backbone RMSD (Å) Medoid model

1 A:2-A:23, A:28-A:104 (99) 0.62 18

Ill-de�ned regions of proteins are excluded from the global statistics.

Ligands and non-protein polymers are included in the analysis.

The models can be grouped into 6 clusters and 1 single-model cluster was found.

Cluster number Models1 1, 7, 8, 10, 14, 202 2, 12, 15, 173 3, 11, 184 9, 165 4, 56 13, 19

Single-model clusters 6

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#ensemble_composition


3 Entry composition iO

There is only 1 type of molecule in this entry. The entry contains 1896 atoms, of which 935 arehydrogens and 0 are deuteriums.

� Molecule 1 is a protein called Photosystem II reaction center psb28 protein.

Mol Chain Residues Atoms Trace

1 A 120Total C H N O S1896 606 935 166 184 5

0

There are 8 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 113 LEU - expression tag UNP Q55356A 114 GLU - expression tag UNP Q55356A 115 HIS - expression tag UNP Q55356A 116 HIS - expression tag UNP Q55356A 117 HIS - expression tag UNP Q55356A 118 HIS - expression tag UNP Q55356A 119 HIS - expression tag UNP Q55356A 120 HIS - expression tag UNP Q55356

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


4 Residue-property plots iO

4.1 Average score per residue in the NMR ensemble

These plots are provided for all protein, RNA and DNA chains in the entry. The �rst graphic is thesame as shown in the summary in section 1 of this report. The second graphic shows the sequencewhere residues are colour-coded according to the number of geometric quality criteria for whichthey contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretchesof 2 or more consecutive residues without any outliers are shown as green connectors. Residueswhich are classi�ed as ill-de�ned in the NMR ensemble, are shown in cyan with an underlinecolour-coded according to the previous scheme. Residues which were present in the experimentalsample, but not modelled in the �nal structure are shown in grey.

• Molecule 1: Photosystem II reaction center psb28 protein

Chain A:

M1

A2

K8

A11

E12

T13

V14

S23

K24

N25

G26

Q27

S28

E37

P38

T39

I55

D56

D57

N72

Q87

P88

E89

W90

N104

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120

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


Chain A:

M1

A2

E3

I4

Q5

F6

S7

K8

G9

K24

N25

G26

Q27

S28

E37

P38

T39

I40

L41

M52

I55

E60

I61

E79

A80

N85

E89

R99

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120



Chain A:

M1

A2

E3

S7

K8

G9

V10

A11

S23

K24

N25

G26

Q27

L36

E37

I55

D56

D57

E58

I78

E79

I83

L84

N85

S86

Q87

P88

E89

W90

R95

F96

M97

E98

R99

Y100

N104

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120

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




Chain A:

M1

A2

Q5

F6

S7

V10

A11

S23

K24

N25

G26

Q27

S28

L36

E37

I49

T50

G51

I55

D56

I71

N72

G73

L84

Q87

P88

E89

W90

F96

Y100

E103

N104

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120



Chain A:

M1

A2

E12

E17

V18

R19

S23

K24

N25

G26

Q27

S28

F33

L36

E37

P38

T39

E44

D48

Y53

L54

I55

D56

D57

E58

G59

E60

I61

I71

N72

G73

R74

P75

T76

A77

I78

E79

Q87

P88

E89

F96

R99

Y100

N104

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120



Chain A:

M1

A2

E3

I4

Q5

F6

S7

A11

E12

T13

K24

N25

G26

Q27

S28

T46

I55

D56

D57

E60

E65

V66

F70

I71

R74

P75

T76

A77

I78

E79

N85

S86

Q87

P88

E89

W90

F96

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120



Chain A:

M1

A2

G9

V10

V14

V15

P16

E17

K24

N25

G26

Q27

L36

E37

P38

T39

I40

E44

D47

D48

I55

D56

D57

E58

I62

T63

R64

E65

I71

N72

G73

R74

P75

T76

Q87

P88

F96

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120




Chain A:

M1

L20

K24

N25

G26

Q27

L36

E37

D47

D48

I49

T50

L54

I55

E58

T63

F70

P75

I83

S86

Q87

P88

E89

W90

M94

Y100

N104

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120



Chain A:

M1

A2

K8

E12

T13

V14

V15

P16

E17

V18

R19

L20

K24

N25

G26

Q27

S28

F33

E37

P38

T39

T50

D56

D57

I71

N72

G73

N85

S86

Q87

P88

R92

M97

E98

G101

A102

E103

N104

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120



Chain A:

M1

A2

E3

E12

T13

V14

K24

N25

G26

Q27

F35

L54

I55

D56

D57

E58

T63

R64

E65

I71

N72

G73

I83

L84

N85

S86

Q87

P88

Y100

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120



Chain A:

M1

A2

E3

I4

Q5

T13

V14

V15

P16

E17

L20

K24

N25

G26

Q27

F35

L36

E37

P38

T39

I40

E44

M52

Y53

L54

I55

D56

D57

E58

I62

E65

K69

F70

I71

N72

G73

E79

I83

Q87

P88

E89

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120




Chain A:

M1

A2

E3

I4

Q5

F6

S7

V10

A11

E12

T13

V14

L20

S21

K24

N25

G26

Q27

S28

K32

L36

E37

P38

T39

I40

L41

L54

I55

D56

D57

E58

G59

E60

I71

N72

G73

I78

E79

A80

I83

L84

N85

S86

Q87

P88

E89

W90

D91

R92

M97

G101

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120



Chain A:

M1

A2

E3

S7

K8

A11

E12

T13

V14

V15

L20

S23

K24

N25

G26

Q27

S28

F35

L36

E37

P38

T39

D56

N85

S86

Q87

P88

F96

Y100

N104

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120



Chain A:

M1

A2

E3

I4

Q5

F6

S7

K8

G9

E12

T13

V14

S23

K24

N25

G26

Q27

S28

E37

P38

T39

I40

E44

S45

T46

I55

D56

D57

E60

I61

I62

I78

E79

A80

N85

F96

E103

N104

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120



Chain A:

M1

V14

V15

P16

E17

V18

K22

S23

K24

N25

G26

Q27

P38

T39

I40

D47

D48

I49

T50

D57

R64

I83

L84

Q87

P88

E89

W90

Y100

N104

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120




Chain A:

M1

Q5

F6

G9

V10

A11

E12

T13

V14

E17

L20

K24

N25

G26

Q27

S28

K32

T39

T50

Y53

L54

I55

D56

D57

E58

G59

T81

L84

Q87

P88

E89

W90

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120



Chain A:

M1

K8

G9

V10

S23

K24

N25

G26

Q27

S28

L36

E37

I49

T50

D56

D57

E58

I71

N72

G73

R74

I83

L84

Q87

P88

E89

W90

R99

Y100

N104

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120



Chain A:

M1

A2

Q5

K8

G9

V10

A11

E12

T13

V14

V15

S23

K24

N25

G26

Q27

S28

G29

E37

P38

T39

Y53

D56

D57

E58

G59

E60

I61

I62

N85

S86

Q87

P88

M97

E98

R99

E103

N104

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120

4.2.18 Score per residue for model 18 (medoid)


Chain A:

M1

A2

G9

V10

V14

V15

K22

S23

K24

N25

G26

Q27

S28

L36

E37

S45

D48

I49

T50

G51

L54

I55

D56

D57

E58

G59

E60

P75

Q87

P88

R92

F96

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120




Chain A:

M1

A2

S7

K8

E12

T13

V14

V15

P16

E17

V18

R19

L20

S23

K24

N25

G26

Q27

F35

T39

I40

L41

D56

D57

E58

G59

I62

E65

K69

T76

A77

I78

E79

I83

Q87

P88

E89

W90

F96

Y100

G101

N104

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120



Chain A:

M1

Q5

F6

S7

K8

G9

V10

A11

E12

T13

L20

S21

K22

S23

K24

N25

G26

Q27

P38

T39

I40

T50

G51

M52

Y53

L54

I55

D56

D57

I71

N72

Q87

P88

F96

G105

L106

G107

F108

S109

K110

S111

E112

L113

E114

H115

H116

H117

H118

H119

H120


5 Re�nement protocol and experimental data overview iO

The models were re�ned using the following method: simulated annealing.

Of the 150 calculated structures, 20 were deposited, based on the following criterion: structures

with the lowest energy.

The following table shows the software used for structure solution, optimisation and re�nement.

Software name Classi�cation VersionX-PLOR NIH structure solution 2.20CNS re�nement 1.2PSVS re�nement 1.4PDBSTAT structure solution 5.1

No chemical shift data was provided. No validations of the models with respect to experimentalNMR restraints is performed at this time.

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#refinement_protocol


6 Model quality iO

6.1 Standard geometry iO

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 iO

In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in each chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashesaveraged over the ensemble.

Mol Chain Non-H H(model) H(added) Clashes1 A 788 780 780 20±5All All 15760 15600 15600 403

The all-atom clashscore is de�ned as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 13.

All unique clashes are listed below, sorted by their clash magnitude.

Atom-1 Atom-2 Clash(Å) Distance(Å)Models

Worst Total

1:A:20:LEU:N 1:A:20:LEU:HD22 0.81 1.90 19 41:A:62:ILE:HD12 1:A:62:ILE:N 0.76 1.95 6 31:A:62:ILE:N 1:A:62:ILE:HD12 0.75 1.96 10 2

1:A:55:ILE:HD12 1:A:55:ILE:N 0.73 1.98 11 91:A:71:ILE:HD12 1:A:71:ILE:N 0.73 1.99 5 11:A:55:ILE:N 1:A:55:ILE:HD12 0.69 2.02 3 41:A:83:ILE:N 1:A:83:ILE:HD12 0.65 2.05 7 31:A:87:GLN:N 1:A:88:PRO:HD2 0.62 2.09 4 5

1:A:14:VAL:HG22 1:A:15:VAL:N 0.62 2.09 12 11:A:20:LEU:N 1:A:20:LEU:CD2 0.61 2.63 19 4

1:A:14:VAL:HG22 1:A:15:VAL:H 0.61 1.55 12 11:A:100:TYR:CE1 1:A:104:ASN:ND2 0.60 2.69 14 41:A:60:GLU:N 1:A:92:ARG:NH2 0.60 2.50 18 11:A:87:GLN:N 1:A:88:PRO:CD 0.59 2.65 2 13

Continued on next page...

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

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

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


Continued from previous page...


Worst Total

1:A:62:ILE:N 1:A:62:ILE:CD1 0.58 2.66 10 21:A:83:ILE:HD12 1:A:83:ILE:N 0.58 2.13 19 21:A:62:ILE:CD1 1:A:62:ILE:N 0.58 2.66 6 21:A:28:SER:CB 1:A:85:ASN:ND2 0.58 2.67 1 11:A:100:TYR:CZ 1:A:104:ASN:ND2 0.58 2.72 14 21:A:20:LEU:HD22 1:A:20:LEU:N 0.57 2.14 7 31:A:72:ASN:HD21 1:A:74:ARG:NE 0.57 1.97 4 11:A:11:ALA:O 1:A:13:THR:N 0.56 2.38 12 11:A:83:ILE:CD1 1:A:83:ILE:N 0.56 2.69 14 11:A:55:ILE:N 1:A:55:ILE:CD1 0.56 2.69 1 81:A:38:PRO:O 1:A:40:ILE:N 0.56 2.39 20 2

1:A:96:PHE:CD1 1:A:99:ARG:NH2 0.55 2.74 2 11:A:83:ILE:N 1:A:83:ILE:CD1 0.55 2.69 16 41:A:17:GLU:N 1:A:17:GLU:OE1 0.55 2.40 4 11:A:87:GLN:H 1:A:87:GLN:CD 0.55 2.05 4 11:A:47:ASP:OD1 1:A:48:ASP:N 0.55 2.40 7 31:A:28:SER:CB 1:A:85:ASN:HD22 0.55 2.15 1 31:A:12:GLU:CD 1:A:12:GLU:H 0.55 2.06 4 11:A:17:GLU:OE1 1:A:17:GLU:N 0.55 2.40 10 21:A:55:ILE:CD1 1:A:55:ILE:N 0.54 2.70 3 41:A:7:SER:OG 1:A:8:LYS:N 0.54 2.39 20 11:A:28:SER:OG 1:A:85:ASN:ND2 0.54 2.41 5 51:A:56:ASP:OD2 1:A:99:ARG:NH2 0.54 2.40 2 11:A:89:GLU:N 1:A:89:GLU:OE1 0.54 2.41 14 11:A:13:THR:O 1:A:14:VAL:O 0.54 2.26 12 61:A:29:GLY:N 1:A:85:ASN:ND2 0.54 2.55 17 1

1:A:55:ILE:HG22 1:A:56:ASP:N 0.54 2.17 6 21:A:56:ASP:OD1 1:A:96:PHE:CD1 0.54 2.61 20 41:A:71:ILE:CD1 1:A:71:ILE:N 0.54 2.70 5 11:A:14:VAL:HG12 1:A:15:VAL:N 0.54 2.18 17 31:A:103:GLU:O 1:A:104:ASN:ND2 0.53 2.41 13 11:A:57:ASP:OD1 1:A:58:GLU:N 0.53 2.41 10 11:A:12:GLU:OE1 1:A:12:GLU:N 0.53 2.41 13 11:A:65:GLU:OE1 1:A:65:GLU:N 0.53 2.42 6 21:A:20:LEU:CD2 1:A:20:LEU:N 0.53 2.71 7 31:A:12:GLU:OE1 1:A:13:THR:N 0.53 2.41 11 11:A:71:ILE:O 1:A:72:ASN:ND2 0.53 2.40 20 1

1:A:3:GLU:OE2 1:A:5:GLN:NE2 0.53 2.42 10 11:A:52:MET:SD 1:A:54:LEU:HD21 0.53 2.44 20 11:A:71:ILE:O 1:A:73:GLY:N 0.53 2.42 6 7

1:A:100:TYR:CZ 1:A:104:ASN:OD1 0.53 2.62 7 1Continued on next page...




Worst Total

1:A:5:GLN:OE1 1:A:9:GLY:N 0.53 2.42 17 11:A:65:GLU:N 1:A:65:GLU:OE1 0.52 2.42 19 1

1:A:20:LEU:HD12 1:A:90:TRP:CZ3 0.52 2.38 7 11:A:96:PHE:CE1 1:A:99:ARG:NH2 0.52 2.78 2 11:A:57:ASP:OD2 1:A:99:ARG:NH1 0.52 2.42 17 11:A:100:TYR:CD1 1:A:104:ASN:OD1 0.52 2.63 19 11:A:103:GLU:N 1:A:103:GLU:OE1 0.52 2.42 3 11:A:56:ASP:OD2 1:A:96:PHE:CE2 0.52 2.62 13 11:A:56:ASP:O 1:A:58:GLU:N 0.52 2.42 16 41:A:10:VAL:O 1:A:11:ALA:HB2 0.52 2.05 3 1

1:A:15:VAL:HG13 1:A:15:VAL:O 0.52 2.04 8 11:A:6:PHE:O 1:A:53:TYR:CD2 0.52 2.63 15 1

1:A:5:GLN:OE1 1:A:10:VAL:N 0.51 2.43 15 11:A:98:GLU:O 1:A:102:ALA:HB2 0.51 2.06 8 11:A:28:SER:CB 1:A:85:ASN:HD21 0.51 2.19 11 11:A:56:ASP:OD1 1:A:92:ARG:NH2 0.51 2.44 11 11:A:56:ASP:OD1 1:A:57:ASP:N 0.51 2.44 15 21:A:57:ASP:O 1:A:59:GLY:N 0.51 2.43 18 4

1:A:56:ASP:OD2 1:A:92:ARG:NH1 0.51 2.43 8 11:A:32:LYS:NZ 1:A:81:THR:OG1 0.51 2.42 15 11:A:5:GLN:NE2 1:A:7:SER:O 0.50 2.44 3 11:A:70:PHE:CD1 1:A:70:PHE:N 0.50 2.80 7 11:A:60:GLU:N 1:A:60:GLU:CD 0.50 2.65 11 2

1:A:95:ARG:NH1 1:A:99:ARG:CZ 0.50 2.75 2 11:A:71:ILE:C 1:A:73:GLY:H 0.50 2.10 16 1

1:A:78:ILE:HG22 1:A:79:GLU:N 0.50 2.21 4 51:A:5:GLN:NE2 1:A:9:GLY:H 0.49 2.05 1 11:A:84:LEU:O 1:A:90:TRP:NE1 0.49 2.46 14 41:A:12:GLU:O 1:A:13:THR:OG1 0.49 2.29 9 51:A:2:ALA:N 1:A:103:GLU:OE2 0.49 2.45 17 1

1:A:72:ASN:HD21 1:A:74:ARG:CD 0.49 2.19 4 11:A:35:PHE:O 1:A:77:ALA:HB1 0.49 2.07 19 11:A:101:GLY:O 1:A:104:ASN:ND2 0.49 2.45 8 11:A:87:GLN:CD 1:A:87:GLN:N 0.49 2.66 2 21:A:12:GLU:O 1:A:13:THR:CB 0.49 2.61 11 11:A:12:GLU:C 1:A:14:VAL:H 0.49 2.10 13 1

1:A:100:TYR:CD1 1:A:104:ASN:ND2 0.49 2.80 14 11:A:23:SER:CB 1:A:28:SER:OG 0.48 2.61 3 11:A:3:GLU:OE1 1:A:13:THR:N 0.48 2.46 9 11:A:84:LEU:O 1:A:90:TRP:CD1 0.48 2.66 3 21:A:79:GLU:CD 1:A:80:ALA:N 0.48 2.67 13 3





Worst Total

1:A:60:GLU:CD 1:A:60:GLU:N 0.48 2.67 5 21:A:56:ASP:OD2 1:A:92:ARG:CZ 0.48 2.62 11 11:A:10:VAL:HG22 1:A:10:VAL:O 0.48 2.07 20 11:A:19:ARG:NH2 1:A:79:GLU:OE2 0.48 2.47 4 11:A:56:ASP:N 1:A:59:GLY:O 0.48 2.46 4 11:A:56:ASP:CG 1:A:57:ASP:N 0.48 2.67 6 31:A:56:ASP:OD1 1:A:96:PHE:CD2 0.48 2.66 12 11:A:49:ILE:O 1:A:51:GLY:N 0.48 2.45 3 2

1:A:55:ILE:CG2 1:A:56:ASP:N 0.48 2.77 13 21:A:8:LYS:C 1:A:10:VAL:H 0.48 2.12 16 11:A:56:ASP:C 1:A:58:GLU:N 0.48 2.67 16 2

1:A:100:TYR:CE2 1:A:104:ASN:OD1 0.48 2.67 4 11:A:12:GLU:CD 1:A:12:GLU:N 0.48 2.67 4 11:A:13:THR:OG1 1:A:14:VAL:N 0.47 2.45 9 11:A:35:PHE:CE1 1:A:52:MET:CE 0.47 2.97 10 11:A:14:VAL:O 1:A:15:VAL:O 0.47 2.33 6 1

1:A:100:TYR:CE1 1:A:104:ASN:OD1 0.47 2.68 19 11:A:38:PRO:C 1:A:40:ILE:N 0.47 2.68 20 31:A:70:PHE:N 1:A:70:PHE:CD1 0.47 2.82 10 11:A:37:GLU:N 1:A:38:PRO:CD 0.47 2.78 10 31:A:5:GLN:NE2 1:A:10:VAL:O 0.47 2.47 3 11:A:83:ILE:HG22 1:A:85:ASN:ND2 0.47 2.24 9 11:A:87:GLN:N 1:A:87:GLN:CD 0.47 2.68 12 11:A:9:GLY:O 1:A:10:VAL:C 0.47 2.53 18 1

1:A:100:TYR:CZ 1:A:104:ASN:CG 0.47 2.88 19 11:A:12:GLU:C 1:A:14:VAL:N 0.46 2.68 13 11:A:49:ILE:O 1:A:49:ILE:HG22 0.46 2.09 16 1

1:A:14:VAL:CG2 1:A:15:VAL:N 0.46 2.77 12 11:A:45:SER:O 1:A:48:ASP:OD1 0.46 2.33 18 1

1:A:63:THR:CG2 1:A:64:ARG:N 0.46 2.77 9 11:A:13:THR:O 1:A:14:VAL:HG12 0.46 2.11 12 11:A:6:PHE:O 1:A:53:TYR:CE2 0.46 2.69 15 11:A:35:PHE:N 1:A:35:PHE:CD1 0.46 2.84 9 1

1:A:18:VAL:HG22 1:A:33:PHE:CE2 0.46 2.46 4 21:A:71:ILE:C 1:A:73:GLY:N 0.46 2.69 6 3

1:A:52:MET:SD 1:A:80:ALA:HB2 0.46 2.51 1 11:A:7:SER:O 1:A:8:LYS:C 0.46 2.53 13 11:A:12:GLU:O 1:A:14:VAL:N 0.46 2.49 19 21:A:10:VAL:O 1:A:11:ALA:C 0.46 2.53 20 11:A:96:PHE:C 1:A:96:PHE:CD1 0.45 2.89 6 11:A:12:GLU:O 1:A:14:VAL:HG23 0.45 2.11 9 1





Worst Total

1:A:15:VAL:N 1:A:16:PRO:CD 0.45 2.79 19 11:A:56:ASP:OD1 1:A:96:PHE:CE2 0.45 2.69 12 11:A:35:PHE:O 1:A:77:ALA:CB 0.45 2.64 19 11:A:40:ILE:O 1:A:44:GLU:N 0.45 2.48 13 2

1:A:57:ASP:OD2 1:A:99:ARG:CZ 0.45 2.64 4 11:A:36:LEU:O 1:A:37:GLU:C 0.45 2.55 6 91:A:2:ALA:HB1 1:A:96:PHE:CE2 0.45 2.46 5 11:A:14:VAL:CG2 1:A:15:VAL:H 0.45 2.24 12 11:A:54:LEU:C 1:A:55:ILE:HD12 0.45 2.33 7 61:A:7:SER:O 1:A:8:LYS:O 0.44 2.35 1 4

1:A:78:ILE:CG2 1:A:79:GLU:N 0.44 2.79 11 31:A:3:GLU:CD 1:A:5:GLN:HE21 0.44 2.13 5 31:A:71:ILE:O 1:A:74:ARG:N 0.44 2.50 6 11:A:56:ASP:O 1:A:56:ASP:OD1 0.44 2.35 9 21:A:12:GLU:CD 1:A:13:THR:N 0.44 2.71 11 11:A:56:ASP:OD2 1:A:99:ARG:CZ 0.44 2.65 2 11:A:56:ASP:OD2 1:A:96:PHE:CD1 0.44 2.69 19 11:A:71:ILE:O 1:A:72:ASN:CG 0.44 2.55 4 31:A:14:VAL:O 1:A:15:VAL:C 0.44 2.55 6 11:A:10:VAL:O 1:A:11:ALA:O 0.44 2.36 11 11:A:64:ARG:O 1:A:65:GLU:C 0.44 2.55 9 11:A:35:PHE:CD1 1:A:35:PHE:N 0.44 2.85 12 11:A:14:VAL:CG1 1:A:15:VAL:N 0.44 2.81 14 21:A:17:GLU:OE2 1:A:18:VAL:O 0.44 2.35 14 11:A:69:LYS:NZ 1:A:79:GLU:OE1 0.44 2.47 19 11:A:21:SER:CB 1:A:32:LYS:HZ3 0.43 2.26 11 11:A:83:ILE:CG2 1:A:85:ASN:OD1 0.43 2.66 11 11:A:71:ILE:O 1:A:72:ASN:C 0.43 2.56 9 5

1:A:63:THR:HG22 1:A:64:ARG:N 0.43 2.28 9 11:A:37:GLU:C 1:A:39:THR:H 0.43 2.16 10 51:A:60:GLU:C 1:A:92:ARG:HH22 0.43 2.17 18 11:A:39:THR:C 1:A:41:LEU:H 0.43 2.16 19 31:A:97:MET:C 1:A:97:MET:SD 0.43 2.96 8 31:A:7:SER:OG 1:A:10:VAL:CG1 0.43 2.66 20 11:A:72:ASN:O 1:A:72:ASN:OD1 0.43 2.36 3 31:A:71:ILE:O 1:A:72:ASN:OD1 0.43 2.37 6 11:A:94:MET:C 1:A:94:MET:SD 0.43 2.96 7 11:A:56:ASP:C 1:A:58:GLU:H 0.43 2.17 2 1

1:A:100:TYR:CE2 1:A:104:ASN:ND2 0.43 2.86 14 11:A:17:GLU:CD 1:A:18:VAL:N 0.43 2.72 14 11:A:97:MET:SD 1:A:97:MET:C 0.43 2.97 17 1





Worst Total

1:A:20:LEU:N 1:A:20:LEU:CD1 0.43 2.81 12 11:A:57:ASP:C 1:A:59:GLY:H 0.43 2.14 18 31:A:87:GLN:CB 1:A:88:PRO:CD 0.43 2.96 19 11:A:13:THR:O 1:A:14:VAL:CG1 0.43 2.67 12 11:A:22:LYS:O 1:A:23:SER:C 0.43 2.57 20 11:A:56:ASP:O 1:A:57:ASP:OD1 0.43 2.36 20 11:A:57:ASP:N 1:A:57:ASP:OD1 0.43 2.52 14 11:A:6:PHE:O 1:A:7:SER:OG 0.42 2.35 5 11:A:40:ILE:O 1:A:44:GLU:O 0.42 2.37 13 2

1:A:72:ASN:OD1 1:A:72:ASN:O 0.42 2.38 9 11:A:83:ILE:O 1:A:89:GLU:OE1 0.42 2.38 10 11:A:56:ASP:CG 1:A:57:ASP:H 0.42 2.17 6 21:A:48:ASP:OD1 1:A:49:ILE:N 0.42 2.51 18 11:A:73:GLY:O 1:A:74:ARG:O 0.42 2.37 16 11:A:57:ASP:O 1:A:57:ASP:OD1 0.42 2.37 5 11:A:103:GLU:O 1:A:104:ASN:O 0.42 2.37 8 11:A:5:GLN:HE22 1:A:9:GLY:H 0.42 1.58 20 11:A:49:ILE:O 1:A:50:THR:C 0.42 2.58 16 1

1:A:100:TYR:CE1 1:A:104:ASN:CG 0.42 2.92 19 11:A:39:THR:C 1:A:41:LEU:N 0.42 2.73 1 31:A:49:ILE:C 1:A:51:GLY:H 0.42 2.17 18 1

1:A:50:THR:OG1 1:A:64:ARG:CZ 0.42 2.67 14 11:A:12:GLU:O 1:A:13:THR:C 0.42 2.57 19 1

1:A:74:ARG:NH2 1:A:76:THR:OG1 0.42 2.53 5 11:A:3:GLU:OE2 1:A:12:GLU:OE2 0.42 2.38 13 11:A:8:LYS:C 1:A:10:VAL:N 0.42 2.72 16 11:A:8:LYS:NZ 1:A:53:TYR:CE2 0.42 2.76 17 11:A:38:PRO:O 1:A:39:THR:C 0.42 2.58 20 1

1:A:44:GLU:OE1 1:A:48:ASP:OD2 0.41 2.37 4 11:A:52:MET:SD 1:A:80:ALA:CB 0.41 3.08 1 11:A:98:GLU:O 1:A:102:ALA:CB 0.41 2.68 8 11:A:64:ARG:N 1:A:65:GLU:OE1 0.41 2.53 6 11:A:12:GLU:O 1:A:13:THR:O 0.41 2.38 8 11:A:23:SER:O 1:A:28:SER:N 0.41 2.54 4 11:A:38:PRO:C 1:A:40:ILE:H 0.41 2.19 14 11:A:53:TYR:N 1:A:53:TYR:CD1 0.41 2.88 4 11:A:65:GLU:O 1:A:66:VAL:O 0.41 2.39 5 11:A:56:ASP:OD1 1:A:56:ASP:O 0.41 2.39 2 11:A:70:PHE:C 1:A:71:ILE:HD12 0.41 2.36 5 1

1:A:48:ASP:OD1 1:A:48:ASP:O 0.41 2.39 6 11:A:61:ILE:HD13 1:A:89:GLU:OE2 0.41 2.16 4 2





Worst Total

1:A:71:ILE:CG1 1:A:76:THR:OG1 0.41 2.69 6 11:A:61:ILE:C 1:A:62:ILE:HD12 0.41 2.35 17 21:A:7:SER:O 1:A:10:VAL:HG23 0.41 2.16 11 11:A:69:LYS:CE 1:A:79:GLU:OE1 0.40 2.69 10 11:A:100:TYR:O 1:A:104:ASN:O 0.40 2.40 3 21:A:79:GLU:OE2 1:A:80:ALA:O 0.40 2.39 11 11:A:56:ASP:CG 1:A:96:PHE:CD2 0.40 2.94 12 11:A:56:ASP:O 1:A:57:ASP:C 0.40 2.60 17 1

1:A:14:VAL:HG12 1:A:15:VAL:H 0.40 1.76 18 1

6.3 Torsion angles iO

6.3.1 Protein backbone iO

In the following table, the Percentiles column shows the percent Ramachandran outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all NMRentries. The Analysed column shows the number of residues for which the backbone conformationwas analysed and the total number of residues.

Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 A 99/120 (82%) 86±3 (86±3%) 9±2 (9±2%) 4±2 (4±2%) 5 30

All All 1980/2400 (82%) 1711 (86%) 186 (9%) 83 (4%) 5 30

All 26 unique Ramachandran outliers are listed below. They are sorted by the frequency ofoccurrence in the ensemble.

Mol Chain Res Type Models (Total)1 A 2 ALA 101 A 14 VAL 81 A 72 ASN 71 A 8 LYS 61 A 9 GLY 61 A 11 ALA 61 A 13 THR 51 A 23 SER 51 A 10 VAL 41 A 12 GLU 31 A 104 ASN 21 A 58 GLU 21 A 28 SER 2


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

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



Mol Chain Res Type Models (Total)1 A 49 ILE 21 A 76 THR 21 A 75 PRO 21 A 57 ASP 21 A 74 ARG 11 A 15 VAL 11 A 66 VAL 11 A 40 ILE 11 A 65 GLU 11 A 39 THR 11 A 45 SER 11 A 38 PRO 11 A 56 ASP 1

6.3.2 Protein sidechains iO

In the following table, the Percentiles column shows the percent sidechain outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all NMRentries. The Analysed column shows the number of residues for which the sidechain conformationwas analysed and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles

1 A 85/103 (83%) 83±1 (98±1%) 2±1 (2±1%) 56 93

All All 1700/2060 (83%) 1665 (98%) 35 (2%) 56 93

All 15 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 87 GLN 71 A 86 SER 61 A 50 THR 51 A 90 TRP 41 A 39 THR 21 A 46 THR 21 A 63 THR 11 A 97 MET 11 A 14 VAL 11 A 89 GLU 11 A 22 LYS 11 A 98 GLU 1


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



Mol Chain Res Type Models (Total)1 A 103 GLU 11 A 94 MET 11 A 104 ASN 1

6.3.3 RNA iO

There are no RNA molecules in this entry.

6.4 Non-standard residues in protein, DNA, RNA chains iO

There are no non-standard protein/DNA/RNA residues in this entry.

6.5 Carbohydrates iO

There are no carbohydrates in this entry.

6.6 Ligand geometry iO

There are no ligands in this entry.

6.7 Other polymers iO

There are no such molecules in this entry.

6.8 Polymer linkage issues iO

There are no chain breaks in this entry.

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

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




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


7 Chemical shift validation iO

No chemical shift data were provided

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#chemical_shifts

full wwpdb nmr structure validation report o...

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