Full wwPDB NMR Structure Validation Report O i...S1 K24 R34 K35 L36 N53 E56 H59 R64 R71 R72 H73 D74...

Full wwPDB NMR Structure Validation Report iO

May 28, 2020 � 09:59 pm BST

PDB ID : 2GF5Title : Structure of intact FADD (MORT1)

Authors : Carrington, P.E.; Sandu, C.; Wei, Y.; Hill, J.M.; Morisawa, G.; Huang, T.;Gavathiotis, E.; Wei, Y.; Werner, M.H.

Deposited on : 2006-03-21

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

We welcome your comments at [email protected]

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

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

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

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

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

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

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

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

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



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

Full wwPDB NMR Structure Validation Report 2GF5

1 Overall quality at a glance iO

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

The overall completeness of chemical shifts assignment was not calculated.

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

MetricWhole archive(#Entries)

NMR archive(#Entries)

Clashscore 158937 12864Ramachandran outliers 154571 11451

Sidechain outliers 154315 11428

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

Mol Chain Length Quality of chain

1 A 191

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


2 Ensemble composition and analysis iO

This entry contains 25 models. Model 22 is the overall representative, medoid model (most similarto other models). The authors have identi�ed model 1 as representative.

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

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

1 A:2-A:190 (189) 0.80 22

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

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

The models can be grouped into 7 clusters and 1 single-model cluster was found.

Cluster number Models1 10, 11, 14, 18, 232 5, 7, 8, 203 13, 15, 17, 214 2, 6, 225 1, 19, 246 9, 12, 167 3, 4

Single-model clusters 25

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 3036 atoms, of which 1527 arehydrogens and 0 are deuteriums.

� Molecule 1 is a protein called FADD protein.

Mol Chain Residues Atoms Trace

1 A 191Total C H N O S3036 929 1527 282 292 6

0

There are 2 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 1 SER - CLONING ARTIFACT UNP Q13158A 25 TYR PHE ENGINEERED UNP Q13158

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: FADD protein

Chain A:

S1

R30

R34

K35

L36

E37

R38

G42

N53

E56

R64

R71

R72

H73

D74

R77

R78

F101

N102

K110

R113

R114

R117

K120

R132

R135

T138

E139

R140

V141

R142

R146

R166

Q169

M170

R184

R189

S190

G191

4.2 Scores per residue for each member of the ensemble

Colouring as in section 4.1 above.

4.2.1 Score per residue for model 1


Chain A:

S1

S16

C27

R30

R34

K35

L36

E37

R38

L49

R64

R71

R72

H73

D74

R77

L97

F101

N102

R117

Q118

I129

R135

T138

E139

R140

R146

E152

K153

H160

R166

M170

R184

N188

R189

S190

G191



Chain A:

S1

D2

S16

R30

K33

R34

K35

L36

E37

R38

G42

N53

H59

T60

E61

L62

R72

R77

R78

V79

D80

A87

F101

N102

R113

R114

L119

K120

I129

R132

Y133

P134

R135

R140

V141

R142

R146

L165

R166

Q169

M170

N171

L172

V173

L186

R189

S190

G191

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




Chain A:

S1

E19

K24

Y25

R30

R34

K35

L36

E37

R38

G42

L43

D44

N53

E56

R64

A68

R71

R72

H73

D74

R77

L97

F101

N102

C105

R114

L119

R140

V141

R142

E154

A164

L165

R166

Q169

R184

G191



Chain A:

S1

R30

K33

R34

K35

L36

E37

R38

V39

Q40

E51

Q52

N53

R64

R71

R72

R77

R78

G89

D96

L97

N102

K110

R114

R117

K120

I126

I129

R132

T138

E139

R140

V141

R142

R146

E152

T157

H160

R166

M170

R184

N188

R189

S190

G191



Chain A:

S1

D2

L15

R30

R34

K35

L36

E37

R38

V39

Q40

L45

Q52

L55

R64

R71

R72

R77

F101

N102

K110

R113

R114

D123

T124

K125

R135

N150

E154

R166

M170

V173

D185

R189

S190

G191



Chain A:

S1

L5

H9

R30

L36

E37

R38

L49

N53

D54

L55

R64

R71

R78

F101

N102

R113

R114

K120

R132

R135

T138

E139

R140

V141

R142

R146

N150

R166

Q169

M170

R189

S190

G191



Chain A:


S1

L5

H9

S10

V11

S12

C27

R30

K33

R34

K35

R38

G42

N53

R64

R71

R72

H73

D74

R77

R78

D81

A87

A88

P92

C105

R114

R117

Q118

L119

K120

R132

R135

R140

R146

N150

T151

E152

K153

E154

T157

H160

L165

R166

Q169

M170

R184

Q187

N188

R189

S190

G191



Chain A:

S1

D2

R34

K35

L36

E37

R38

V39

Q40

L43

D44

L45

H59

R64

R71

R77

R78

A90

F101

N102

D111

W112

R113

R114

R117

K120

N136

R140

V141

R142

R146

R166

Q169

M170

Q182

L186

R189

S190

G191



Chain A:

S1

L5

H9

S18

E22

L23

K24

Y25

L26

C27

R30

R34

K35

L36

E56

R64

S69

L70

R71

R72

L97

F101

N102

K110

R113

R114

R117

S122

I126

I129

R132

E139

R140

V141

R142

R146

K153

L165

R166

Q169

M170

R184

G191



Chain A:

S1

D2

S18

Y25

R30

R34

K35

L36

G42

N53

E56

R64

R71

R72

H73

D74

R77

R78

A87

N102

R117

Q118

L119

K120

R132

R135

T138

E139

R140

V141

R142

R166

L172

L186

R189

S190

G191



Chain A:

S1

D2

L5

H9

Y25

R30

K33

L36

L43

E51

E56

P57

G58

R71

R72

H73

D74

L75

L76

R77

R78

V79

D80

D96

N102

D111

W112

R113

R117

Q118

R132

R135

R142

R146

R166

Q169

R184

R189


S190

G191



Chain A:

S1

S16

S17

L23

K24

R34

K35

L36

Q40

S41

G42

L43

D44

N53

E56

R64

R71

R72

H73

R77

R78

A91

F101

N102

D111

W112

R113

R114

L115

S122

R135

T138

E139

R140

S144

R166

Q169

M170

R184

N188

R189

S190

G191



Chain A:

S1

L5

H9

S18

L26

R34

K35

L36

E37

R38

S41

G42

H59

R64

R71

R72

H73

D74

R77

R78

A88

F101

N102

C105

R113

R117

K120

I126

R132

R135

R142

R146

N150

K153

R166

Q169

M170

E179

R184

D185

L186

R189

S190

G191



Chain A:

S1

K24

R34

K35

L36

N53

E56

H59

R64

R71

R72

H73

D74

R77

R78

F101

N102

R114

R117

Q118

I126

T138

R142

R146

K153

H160

R166

M170

Q181

R184

D185

R189

S190

G191



Chain A:

S1

L5

H9

L23

C27

K33

L36

G42

L43

E56

H59

R64

R71

D74

R77

R78

L97

F101

C105

K110

R113

R114

L115

K120

D131

R132

R146

K153

E154

A164

L165

R166

M170

L186


R189

S190

G191



Chain A:

S1

D2

L15

L28

G29

R30

R34

K35

L36

E37

R38

N53

E61

R64

R71

R77

R78

V79

D80

L97

F101

N102

C105

K110

R113

R117

Q118

L119

K120

I126

I129

R132

Y133

P134

R135

T138

R142

R146

A156

T157

L165

R166

M170

R184

N188

R189

S190

G191



Chain A:

S1

E22

R30

K33

R34

K35

L36

E37

R38

N53

E56

H59

R64

E65

R71

R72

H73

D74

L75

L76

R77

R78

A88

F101

N102

K110

D111

W112

R113

R117

Q118

L119

K120

V121

I129

R132

R135

T138

E139

R140

V141

R142

R146

N150

E154

R166

Q169

M170

N171

L172

L186

Q187

N188

R189

S190

G191



Chain A:

S1

D2

L15

Y25

L28

G29

R30

K33

R34

K35

L36

E37

R38

G42

L43

E61

L62

L63

R64

R71

R72

H73

D74

R77

R78

V79

D80

P92

F101

N102

K110

R113

R114

L115

A116

R117

K120

I129

E130

D131

R132

R135

N136

R140

R166

Q169

M170

L176

R184

R189

S190

G191



Chain A:


S1

D2

L5

H9

L26

R30

L36

E37

R38

L43

L50

L55

E56

P57

R64

L70

R71

R72

H73

D74

R78

F82

A86

A91

F101

N102

K110

D111

W112

R113

R114

R117

K120

D123

R132

Y133

P134

R135

T138

E139

R140

V141

R142

R146

E154

Q169

M170

A174

Q181

R184

R189

S190

G191



Chain A:

S1

S16

R30

R34

K35

L36

E37

R38

D44

N53

D54

L55

R64

R71

R78

V79

D80

A87

N102

D111

W112

R113

R114

R117

Q118

L119

K120

D127

R135

V141

R142

R146

E152

K153

E154

T157

R166

Q169

M170

L186

Q187

N188

G191



Chain A:

S1

L5

H9

L15

E22

R30

K33

R34

K35

L36

E37

R38

G42

L43

N53

E61

R64

L70

R71

R72

H73

D74

L75

L76

R77

R78

A87

F101

N102

R113

R114

R117

K120

R132

R135

T138

E139

R140

R146

R166

M170

R184

N188

R189

S190

G191

4.2.22 Score per residue for model 22 (medoid)


Chain A:

S1

S16

R30

R34

R38

G42

Q52

N53

D54

H59

T60

E61

R64

R71

D74

R77

E83

A90

F101

N102

D111

W112

R113

R114

R117

Q118

L119

K120

I129

R132

R135

T138

E139

R140

V141

R142

R146

Q169

R184

D185

L186

Q187

N188

R189

S190

G191




Chain A:

S1

L5

H9

L15

R30

K33

L36

E37

R38

L43

N53

E56

L62

R71

R72

H73

D74

R77

D80

G85

L97

F101

N102

K110

R113

R114

R117

I129

R132

Y133

P134

R135

R140

R146

K153

H160

R166

Q169

M170

R184

R189

S190

G191



Chain A:

S1

D2

E19

R30

K33

R34

R38

V39

Q40

L43

Q52

E56

H59

R71

R72

H73

D74

R77

E95

F101

N102

R113

R114

R117

Q118

D127

R132

Y133

P134

R135

R140

V141

R142

R146

N150

T151

E152

K153

H160

R166

Q169

M170

R184

N188

R189

S190

G191



Chain A:

S1

L5

H9

L15

E19

E22

C27

R30

R34

K35

L36

E37

R38

G42

L43

E51

Q52

N53

H59

R64

R71

R72

H73

D74

R77

E83

N102

K110

R113

R114

R117

Q118

R135

T138

R146

R166

Q169

M170

R189

S190

G191


5 Re�nement protocol and experimental data overview iO

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

Of the 100 calculated structures, 25 were deposited, based on the following criterion: 25 structures

for lowest energy.

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

Software name Classi�cation VersionX-PLOR re�nement 2.12.2X-PLOR structure solution 2.12.2

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

COVALENT-GEOMETRY INFOmissingINFO

5.1 Too-close contacts iO

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

Mol Chain Non-H H(model) H(added) Clashes1 A 1498 1517 1513 2±1All All 37450 37925 37825 38

The all-atom clashscore is de�ned as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 1.

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

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

Worst Total

1:A:5:LEU:O 1:A:9:HIS:CD2 0.52 2.63 11 101:A:9:HIS:CD2 1:A:43:LEU:HD11 0.51 2.41 23 3

1:A:165:LEU:HD11 1:A:173:VAL:HG23 0.49 1.84 2 11:A:59:HIS:CE1 1:A:83:GLU:OE1 0.49 2.65 22 11:A:112:TRP:CD1 1:A:141:VAL:HG12 0.49 2.42 20 11:A:59:HIS:CD2 1:A:154:GLU:HG2 0.48 2.44 15 11:A:56:GLU:OE2 1:A:59:HIS:CD2 0.47 2.67 24 21:A:73:HIS:CE1 1:A:74:ASP:OD2 0.47 2.68 23 21:A:97:LEU:HD21 1:A:156:ALA:HB3 0.47 1.84 16 11:A:152:GLU:OE2 1:A:160:HIS:CE1 0.46 2.69 24 2

Continued on next page...

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

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


Continued from previous page...

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

Worst Total

1:A:119:LEU:HD21 1:A:164:ALA:HB2 0.46 1.87 3 11:A:55:LEU:H 1:A:55:LEU:CD2 0.45 2.24 20 11:A:82:PHE:HA 1:A:86:ALA:HB3 0.45 1.88 19 11:A:59:HIS:CD2 1:A:154:GLU:OE2 0.44 2.71 17 11:A:118:GLN:O 1:A:160:HIS:CE1 0.43 2.71 14 1

1:A:115:LEU:HD11 1:A:164:ALA:HA 0.43 1.91 15 11:A:111:ASP:HA 1:A:113:ARG:HH11 0.43 1.74 8 11:A:75:LEU:O 1:A:79:VAL:HG23 0.43 2.13 11 11:A:59:HIS:CE1 1:A:83:GLU:HB3 0.43 2.49 25 11:A:52:GLN:HA 1:A:52:GLN:HE21 0.42 1.73 5 11:A:152:GLU:OE1 1:A:160:HIS:CD2 0.42 2.71 7 11:A:73:HIS:CE1 1:A:74:ASP:OD1 0.42 2.73 18 11:A:133:TYR:CG 1:A:139:GLU:HG3 0.41 2.50 19 11:A:157:THR:OG1 1:A:160:HIS:CD2 0.41 2.74 4 1

5.2 Torsion angles iO

5.2.1 Protein backbone iO

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

Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 A 189/191 (99%) 165±3 (87±2%) 21±3 (11±2%) 3±1 (2±1%) 13 56

All All 4725/4775 (99%) 4128 (87%) 518 (11%) 79 (2%) 13 56

All 27 unique Ramachandran outliers are listed below. They are sorted by the frequency ofoccurrence in the ensemble.

Mol Chain Res Type Models (Total)1 A 169 GLN 121 A 42 GLY 101 A 53 ASN 81 A 120 LYS 61 A 87 ALA 51 A 110 LYS 51 A 27 CYS 31 A 16 SER 3


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 33 LYS 31 A 71 ARG 31 A 153 LYS 21 A 28 LEU 21 A 72 ARG 21 A 126 ILE 21 A 154 GLU 11 A 58 GLY 11 A 43 LEU 11 A 134 PRO 11 A 123 ASP 11 A 121 VAL 11 A 44 ASP 11 A 112 TRP 11 A 122 SER 11 A 172 LEU 11 A 73 HIS 11 A 68 ALA 11 A 90 ALA 1

5.2.2 Protein sidechains iO

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

Mol Chain Analysed Rotameric Outliers Percentiles

1 A 165/166 (99%) 149±3 (90±2%) 16±3 (10±2%) 12 58

All All 4125/4150 (99%) 3730 (90%) 395 (10%) 12 58

All 92 unique residues with a non-rotameric sidechain are listed below. They are sorted by thefrequency of occurrence in the ensemble.

Mol Chain Res Type Models (Total)1 A 102 ASN 231 A 36 LEU 221 A 71 ARG 151 A 74 ASP 121 A 138 THR 121 A 77 ARG 10


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



Mol Chain Res Type Models (Total)1 A 56 GLU 101 A 188 ASN 101 A 101 PHE 101 A 170 MET 91 A 129 ILE 91 A 118 GLN 91 A 53 ASN 81 A 33 LYS 81 A 120 LYS 81 A 186 LEU 81 A 30 ARG 71 A 114 ARG 71 A 169 GLN 71 A 2 ASP 71 A 150 ASN 61 A 97 LEU 61 A 153 LYS 61 A 15 LEU 61 A 43 LEU 51 A 184 ARG 51 A 113 ARG 51 A 105 CYS 51 A 61 GLU 51 A 126 ILE 51 A 73 HIS 51 A 154 GLU 41 A 35 LYS 41 A 80 ASP 41 A 34 ARG 41 A 52 GLN 31 A 59 HIS 31 A 172 LEU 31 A 19 GLU 31 A 55 LEU 31 A 189 ARG 31 A 24 LYS 31 A 23 LEU 31 A 165 LEU 31 A 110 LYS 31 A 140 ARG 31 A 62 LEU 31 A 27 CYS 3




Mol Chain Res Type Models (Total)1 A 117 ARG 31 A 51 GLU 31 A 92 PRO 21 A 131 ASP 21 A 16 SER 21 A 132 ARG 21 A 111 ASP 21 A 18 SER 21 A 135 ARG 21 A 26 LEU 21 A 185 ASP 21 A 45 LEU 21 A 40 GLN 21 A 115 LEU 21 A 127 ASP 21 A 22 GLU 21 A 70 LEU 21 A 96 ASP 21 A 76 LEU 21 A 54 ASP 21 A 49 LEU 21 A 38 ARG 21 A 181 GLN 21 A 119 LEU 21 A 65 GLU 11 A 125 LYS 11 A 11 VAL 11 A 136 ASN 11 A 44 ASP 11 A 190 SER 11 A 95 GLU 11 A 64 ARG 11 A 139 GLU 11 A 142 ARG 11 A 50 LEU 11 A 182 GLN 11 A 179 GLU 11 A 69 SER 11 A 176 LEU 11 A 81 ASP 11 A 123 ASP 11 A 187 GLN 1




Mol Chain Res Type Models (Total)1 A 166 ARG 11 A 173 VAL 1

5.2.3 RNA iO

There are no RNA molecules in this entry.

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

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

5.4 Carbohydrates iO

There are no carbohydrates in this entry.

5.5 Ligand geometry iO

There are no ligands in this entry.

5.6 Other polymers iO

There are no such molecules in this entry.

5.7 Polymer linkage issues iO

There are no chain breaks in this entry.

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


6 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 i...S1 K24 R34 K35 L36 N53 E56 H59 R64 R71 R72 H73 D74...

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