full wwpdb em model validation report i · 2020-06-22 · full wwpdb em model validation report i...

Full wwPDB EM Map/Model Validation Report iO

Aug 10, 2020 � 02:09 AM BST

PDB ID : 6XBDEMDB ID : EMD-22116

Title : Cryo-EM structure of MlaFEDB in nanodiscs with phospholipid substratesAuthors : Coudray, N.; Isom, G.L.; MacRae, M.R.; Saiduddin, M.; Ekiert, D.C.; Bhabha,

G.Deposited on : 2020-06-05Resolution : 3.05 Å(reported)

Based on initial models : 5UW2, 6CM1

This is a Full wwPDB EM Map/Model 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/EMValidationReportHelpwith 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:

EMDB validation analysis : 0.0.0.dev33Mogul : 1.8.5 (274361), CSD as541be (2020)

MolProbity : 4.02b-467buster-report : 1.1.7 (2018)

Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)Ideal geometry (proteins) : Engh & Huber (2001)

Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : 2.13.1

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



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

Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD

1 Overall quality at a glance iO

The following experimental techniques were used to determine the structure:ELECTRON MICROSCOPY

The reported resolution of this entry is 3.05 Å.

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)

EM structures(#Entries)

Clashscore 158937 4297Ramachandran outliers 154571 4023

Sidechain outliers 154315 3826

The table below summarises the geometric issues observed across the polymeric chains and their�t to the map. The red, orange, yellow and green segments on the bar indicate the fraction ofresidues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. Agrey segment represents the fraction of residues that are not modelled. The numeric value for eachfraction is indicated below the corresponding segment, with a dot representing fractions <=5%The upper red bar (where present) indicates the fraction of residues that have poor �t to the EMmap (all atom inclusion < 40%). The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 A 201

1 B 201

1 C 201

1 D 201

1 E 201

1 F 201

2 G 260

2 H 260Continued on next page...

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


Continued from previous page...

Mol Chain Length Quality of chain

3 I 269

3 J 269

4 K 97

4 L 97

5 M 164

5 N 164


2 Entry composition iO

There are 6 unique types of molecules in this entry. The entry contains 17433 atoms, of which 0are hydrogens and 0 are deuteriums.

In the tables below, the AltConf column contains the number of residues with at least one atomin alternate conformation and the Trace column contains the number of residues modelled with atmost 2 atoms.

� Molecule 1 is a protein called Phospholipid ABC transporter-binding protein mlaD.

Mol Chain Residues Atoms AltConf Trace

1 A 144Total C N O S1108 715 178 213 2

0 0

1 B 138Total C N O S1063 687 170 204 2

0 0

1 C 144Total C N O S1033 652 172 208 1

0 0

1 D 143Total C N O S1096 707 177 210 2

0 0

1 E 145Total C N O S1112 718 179 213 2

0 0

1 F 143Total C N O S1028 649 171 207 1

0 0

There are 108 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA -17 MET - expression tag UNP H4UPP8A -16 HIS - expression tag UNP H4UPP8A -15 HIS - expression tag UNP H4UPP8A -14 HIS - expression tag UNP H4UPP8A -13 HIS - expression tag UNP H4UPP8A -12 HIS - expression tag UNP H4UPP8A -11 HIS - expression tag UNP H4UPP8A -10 GLN - expression tag UNP H4UPP8A -9 HIS - expression tag UNP H4UPP8A -8 GLN - expression tag UNP H4UPP8A -7 HIS - expression tag UNP H4UPP8A -6 GLU - expression tag UNP H4UPP8A -5 ASN - expression tag UNP H4UPP8A -4 LEU - expression tag UNP H4UPP8A -3 TYR - expression tag UNP H4UPP8A -2 PHE - expression tag UNP H4UPP8A -1 GLN - expression tag UNP H4UPP8A 0 GLY - expression tag UNP H4UPP8

Continued on next page...

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



Chain Residue Modelled Actual Comment ReferenceB -17 MET - expression tag UNP H4UPP8B -16 HIS - expression tag UNP H4UPP8B -15 HIS - expression tag UNP H4UPP8B -14 HIS - expression tag UNP H4UPP8B -13 HIS - expression tag UNP H4UPP8B -12 HIS - expression tag UNP H4UPP8B -11 HIS - expression tag UNP H4UPP8B -10 GLN - expression tag UNP H4UPP8B -9 HIS - expression tag UNP H4UPP8B -8 GLN - expression tag UNP H4UPP8B -7 HIS - expression tag UNP H4UPP8B -6 GLU - expression tag UNP H4UPP8B -5 ASN - expression tag UNP H4UPP8B -4 LEU - expression tag UNP H4UPP8B -3 TYR - expression tag UNP H4UPP8B -2 PHE - expression tag UNP H4UPP8B -1 GLN - expression tag UNP H4UPP8B 0 GLY - expression tag UNP H4UPP8C -17 MET - expression tag UNP H4UPP8C -16 HIS - expression tag UNP H4UPP8C -15 HIS - expression tag UNP H4UPP8C -14 HIS - expression tag UNP H4UPP8C -13 HIS - expression tag UNP H4UPP8C -12 HIS - expression tag UNP H4UPP8C -11 HIS - expression tag UNP H4UPP8C -10 GLN - expression tag UNP H4UPP8C -9 HIS - expression tag UNP H4UPP8C -8 GLN - expression tag UNP H4UPP8C -7 HIS - expression tag UNP H4UPP8C -6 GLU - expression tag UNP H4UPP8C -5 ASN - expression tag UNP H4UPP8C -4 LEU - expression tag UNP H4UPP8C -3 TYR - expression tag UNP H4UPP8C -2 PHE - expression tag UNP H4UPP8C -1 GLN - expression tag UNP H4UPP8C 0 GLY - expression tag UNP H4UPP8D -17 MET - expression tag UNP H4UPP8D -16 HIS - expression tag UNP H4UPP8D -15 HIS - expression tag UNP H4UPP8D -14 HIS - expression tag UNP H4UPP8D -13 HIS - expression tag UNP H4UPP8D -12 HIS - expression tag UNP H4UPP8




Chain Residue Modelled Actual Comment ReferenceD -11 HIS - expression tag UNP H4UPP8D -10 GLN - expression tag UNP H4UPP8D -9 HIS - expression tag UNP H4UPP8D -8 GLN - expression tag UNP H4UPP8D -7 HIS - expression tag UNP H4UPP8D -6 GLU - expression tag UNP H4UPP8D -5 ASN - expression tag UNP H4UPP8D -4 LEU - expression tag UNP H4UPP8D -3 TYR - expression tag UNP H4UPP8D -2 PHE - expression tag UNP H4UPP8D -1 GLN - expression tag UNP H4UPP8D 0 GLY - expression tag UNP H4UPP8E -17 MET - expression tag UNP H4UPP8E -16 HIS - expression tag UNP H4UPP8E -15 HIS - expression tag UNP H4UPP8E -14 HIS - expression tag UNP H4UPP8E -13 HIS - expression tag UNP H4UPP8E -12 HIS - expression tag UNP H4UPP8E -11 HIS - expression tag UNP H4UPP8E -10 GLN - expression tag UNP H4UPP8E -9 HIS - expression tag UNP H4UPP8E -8 GLN - expression tag UNP H4UPP8E -7 HIS - expression tag UNP H4UPP8E -6 GLU - expression tag UNP H4UPP8E -5 ASN - expression tag UNP H4UPP8E -4 LEU - expression tag UNP H4UPP8E -3 TYR - expression tag UNP H4UPP8E -2 PHE - expression tag UNP H4UPP8E -1 GLN - expression tag UNP H4UPP8E 0 GLY - expression tag UNP H4UPP8F -17 MET - expression tag UNP H4UPP8F -16 HIS - expression tag UNP H4UPP8F -15 HIS - expression tag UNP H4UPP8F -14 HIS - expression tag UNP H4UPP8F -13 HIS - expression tag UNP H4UPP8F -12 HIS - expression tag UNP H4UPP8F -11 HIS - expression tag UNP H4UPP8F -10 GLN - expression tag UNP H4UPP8F -9 HIS - expression tag UNP H4UPP8F -8 GLN - expression tag UNP H4UPP8F -7 HIS - expression tag UNP H4UPP8F -6 GLU - expression tag UNP H4UPP8




Chain Residue Modelled Actual Comment ReferenceF -5 ASN - expression tag UNP H4UPP8F -4 LEU - expression tag UNP H4UPP8F -3 TYR - expression tag UNP H4UPP8F -2 PHE - expression tag UNP H4UPP8F -1 GLN - expression tag UNP H4UPP8F 0 GLY - expression tag UNP H4UPP8

� Molecule 2 is a protein called Phospholipid ABC transporter permease protein mlaE.


2 G 256Total C N O S1926 1261 323 330 12

0 0

2 H 255Total C N O S1918 1257 321 328 12

0 0

� Molecule 3 is a protein called Phospholipid transport system ATP-binding protein MlaF.


3 I 263Total C N O S1996 1268 352 362 14

0 0

3 J 263Total C N O S1996 1268 352 362 14

0 0

� Molecule 4 is a protein called Phospholipid ABC transporter-binding protein mlaB.


4 K 95Total C N O S734 464 124 143 3

0 0

4 L 95Total C N O S734 464 124 143 3

0 0

� Molecule 5 is a protein called MSP1D1.


5 M 164Total C N O821 492 164 165

0 0

5 N 156Total C N O780 468 156 156

0 0

� Molecule 6 is DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE (three-lettercode: PEF) (formula: C37H74NO8P) (labeled as "Ligand of Interest" by author).


Mol Chain Residues Atoms AltConf

6 G 1Total C O P88 70 16 2

0

6 G 1Total C O P88 70 16 2

0


3 Residue-property plots iO

These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The�rst graphic for a chain summarises the proportions of the various outlier classes displayed in thesecond graphic. The second graphic shows the sequence view annotated by issues in geometry andatom inclusion in map density. Residues are color-coded according to the number of geometricquality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2and red = 3 or more. A red diamond above a residue indicates a poor �t to the EM map forthis residue (all atom inclusion < 40%). Stretches of 2 or more consecutive residues without anyoutlier are shown as a green connector. Residues present in the sample, but not in the model, areshown in grey.

• Molecule 1: Phospholipid ABC transporter-binding protein mlaD

Chain A:

MET

HIS

HIS

HIS

HIS

HIS

HIS

GLN

HIS

GLN

HIS

GLU

ASN

LEU

TYR

PHE

GLN

GLY

MET

Q2

�

K27

A28

ALA

ASN

VAL

THR

SER

ILE

ARG

T36

Y40

T41

L42

Y43

D47

N48

I49

R55

I60

V65

I71

K76

V82

T83

L84

E85

I86

E87

Q88

N91

R102

L106

E122�

T133

L146

Y152

GLY

SER

LYS

GLY

ASP

ASP

ASN

LYS

ASN

SER

GLY

ASP

ALA

PRO

ALA

ALA

ALA

PRO

GLY

ASN

ASN

GLU

THR

THR

GLU

PRO

VAL

GLY

THR

THR

LYS


Chain B:

MET

HIS

HIS

HIS

HIS

HIS

HIS

GLN

HIS

GLN

HIS

GLU

ASN

LEU

TYR

PHE

GLN

GLY

MET

GLN

THR

K4

E7

V10

L18

�

L22

�F23

V24

�C25

LEU

LYS

ALA

ALA

ASN

VAL

THR

SER

ILE

ARG

THR

E37

P38

T39

I49

K53

A54

R55

A69

D70

I71

T83

E87

Q88

N91

D95

T103

L107

Q110

Y111

L112

E119

D120�

P121�

E122�

L123

G124�

T125

A126

I127

L128

D132

T133

V142

D145

Q149

Y152

GLY

SER

LYS

GLY

ASP

ASP

ASN

LYS

ASN

SER

GLY

ASP

ALA

PRO

ALA

ALA

ALA

PRO

GLY

ASN

ASN

GLU

THR

THR

GLU

PRO

VAL

GLY

THR

THR

LYS


Chain C:

MET

HIS

HIS

HIS

HIS

HIS

HIS

GLN

HIS

GLN

HIS

GLU

ASN

LEU

TYR

PHE

GLN

GLY

MET

GLN

THR

K4

K5

�

L14

�L15

A16

�A17

L18

�L19

�A20

A21

�L22

�

N30

VAL

THR

SER

ILE

ARG

T36

E37

F46

D47

N48

I49

L52

V58

V68

A69

D70

I71

T83

P94

D95

L99

S100

I101

L112

E119

D120

P121�

E122�

L123

G124�

K129

D130

G131

D132

S139

V142

L143

E144

D145

Y152

GLY

SER

LYS

GLY

ASP

ASP

ASN

LYS

ASN

SER

GLY

ASP

ALA

PRO

ALA

ALA

ALA

PRO

GLY

ASN

ASN

GLU

THR

THR

GLU

PRO

VAL

GLY

THR

THR

LYS


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


Chain D:

MET

HIS

HIS

HIS

HIS

HIS

HIS

GLN

HIS

GLN

HIS

GLU

ASN

LEU

TYR

PHE

GLN

GLY

MET

Q2

K5

K27

A28

A29

ASN

VAL

THR

SER

ILE

ARG

T36

E37

I49

A69

D70

I71

T72

L73

T83

R102

P121

GLU

LEU

G124

D132

T133

V142

Y152

GLY

SER

LYS

GLY

ASP

ASP

ASN

LYS

ASN

SER

GLY

ASP

ALA

PRO

ALA

ALA

ALA

PRO

GLY

ASN

ASN

GLU

THR

THR

GLU

PRO

VAL

GLY

THR

THR

LYS


Chain E:

MET

HIS

HIS

HIS

HIS

HIS

HIS

GLN

HIS

GLN

HIS

GLU

ASN

LEU

TYR

PHE

GLN

GLY

MET

GLN

THR

K4

I8

I12

C25

A29

N30

V31

�THR

SER

ILE

ARG

T36

E37

�P38

T39

I49

V63

A69

D70

I71

T77

Y78

L79

V82

T83

Q88

R102

T103

L107

Q110

P121�

E122�

L123�

K129

D132

T133

Y152

GLY

SER

LYS

GLY

ASP

ASP

ASN

LYS

ASN

SER

GLY

ASP

ALA

PRO

ALA

ALA

ALA

PRO

GLY

ASN

ASN

GLU

THR

THR

GLU

PRO

VAL

GLY

THR

THR

LYS


Chain F:

MET

HIS

HIS

HIS

HIS

HIS

HIS

GLN

HIS

GLN

HIS

GLU

ASN

LEU

TYR

PHE

GLN

GLY

MET

GLN

THR

K4

K5

�N6

E7

�

V10

�

L14

�L15

�A16

A17

�L18

�L19

�A20

�A21

�L22

�F23

�V24

C25

�L26

�K27

�A28

�A29

ASN

VAL

THR

SER

ILE

ARG

T36

E37

P38

I49

K53

I71

Q88

R89

I101

L106

L112

D120�

P121

E122�

L123�

G124�

K129

D132

V142

L143

E144

D145

L146

I147

Y152

GLY

SER

LYS

GLY

ASP

ASP

ASN

LYS

ASN

SER

GLY

ASP

ALA

PRO

ALA

ALA

ALA

PRO

GLY

ASN

ASN

GLU

THR

THR

GLU

PRO

VAL

GLY

THR

THR

LYS

• Molecule 2: Phospholipid ABC transporter permease protein mlaE

Chain G:

MET

LEU

LEU

N4

R18

R22

L25

K34

�P35

E36

F37

R38

�

I58

I66

L70

Q73

Y81

M89

L90

L93

S94

E98

L99

G100

V103

G113

S114

E119

T126

R141

R147

L155

F162

W168

L172

M189

Q190

N191

A192

V193

D194

W195

R196

M197

D198

A210

S217

D223

S232

T235

V240

L244

T254

G259

ASN

• Molecule 2: Phospholipid ABC transporter permease protein mlaE

Chain H:

MET

LEU

LEU

ASN

A5

G10

K34

�P35

E36

F37

R38

K39

H40

Y49

S55

I58

L70

Y75

S82

L90

L93

E98

L99

G100

F108

G113

S114

A118

E119

M135

P139

L140

R141

R142

V143

I144

S145

P146

R147

F148

W149

L155


F162

W168

L172

W177

V193

D194

K205

A210

I225

P226

T227

G230

T235

V240

L256

M257

F258

G259

ASN

• Molecule 3: Phospholipid transport system ATP-binding protein MlaF

Chain I:

MET

GLU

GLN

SER

V5

D13

C22

S28

I39

M40

I45

T49

L50

L51

R52

L53

I58

F67

I72

M87

A95

M100

N101

D104

N105

V106

K128

L129

E130

A131

R135

G136

A137

L140

S146

G147

R151

R157

A160

L165

I166

M167

E170

P171

G181

V184

V201

S202

H203

L209

L218

K221

L232

R241

Q242

V252

R255

G259�

D260

L266

P267

GLY

SER

• Molecule 3: Phospholipid transport system ATP-binding protein MlaF

Chain J:

MET

GLU

GLN

SER

V5

�

D13

C22

S28

I39

M40

I45

T49

L50

L51

R52

L53

I58

F67

I72

K85

R86

M87

Q92

A95

M100

D104

N105

V106

H113

K128

L129

E130

A131

R135

G136

A137

L140

S146

G147

R151

R157

A160

L165

I166

M167

E170

P171

G181

V184

V201

S202

H203

L209

L218

K221

L232

R241

Q242

V252

R255

D260

P267

GLY

SER

• Molecule 4: Phospholipid ABC transporter-binding protein mlaB

Chain K:

MET

SER

E3

S6

W7

L14

S17

D21

Q22

D23

V24

L25

L26

E30

I39

L44

D51

L55

L59

I62

K66

N70

L74

V77

K80

V81

Y82

A85

Y88

N89

L90

D93

V94

L95

P96

R97

• Molecule 4: Phospholipid ABC transporter-binding protein mlaB

Chain L:

MET

SER

E3

S6

W7

L14

S17

D21

Q22

D23

V24

L25

L26

E30

I39

L44

D51

L55

L59

I62

D63

K66

N70

L74

V77

K80

V81

A85

Y88

N89

L90

D93

V94

L95

P96

R97

• Molecule 5: MSP1D1

Chain M:

X1

�X2

X3

�X4

�X5

�X6

�X7

�X8

X9

X12

�X13

�

X25

X29

X36

�

X42

�

X52

�X53

X54

�

X58

�X59

X60

�X61

X62

�X63

X64

�X65

�X66

X67

�X68

�X69

�X70

X71

�X72

�X73

X74

�X75

X76

�X77

�X78

X79

�X80

�X81

�X82

X83

�X84

X85

�X86

�X87

�X88

X89

X90

�X91

�X92

X95

�

X99

X100

X101�

X102

X103�

X106

X122�

X126�

X127

X128

X129�

X130

X131

X132

X133

X134

X137

X138

X142

X146

X147�

X150�

X151�

X152�

X153�

X154�

X155�

X156�

X157�

X158�

X159�

X160�

X161�

X162�

X163

X164�


• Molecule 5: MSP1D1

Chain N:

X1

�X2

�X3

�X4

X5

�X6

X7

�

X12

�X13

�X14

X15

�

X27

�

X30

�X31

X32

�X33

X34

X37

X41

X42

X45

X46

X49

X52

X56

X62

X65

�X66

�X67

X68

X69

�X70

�X71

X72

X73

�X74

X75

X76

�X77

X78

X79

X80

�X81

X82

X83

�X84

�X85

X86

�X87

�

X88

X89

X90

X91

�

X94

�X95

X96

X97

�X98

X99

X100

X101

X102

X103

X104�

X105

X106�

X107

X108�

X109

X112�

X113�

X117�

X118

X119�

X126

X130

X134

X138�

X139�

X140

X141�

X142�

X143�

X144�

X145�

X146�

X147�

X148�

X149�

X150�

X151�

X152

X153�

X154�

X155

X156

UNK

UNK

UNK

UNK

UNK

UNK

UNK

UNK


4 Experimental information iO

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C1 DepositorNumber of particles used 731205 DepositorResolution determination method FSC 0.143 CUT-OFF DepositorCTF correction method PHASE FLIPPING AND AMPLITUDE

CORRECTIONDepositor

Microscope FEI TITAN KRIOS DepositorVoltage (kV) 300 DepositorElectron dose (e−/Å

2) 71 Depositor

Minimum defocus (nm) Not provided DepositorMaximum defocus (nm) Not provided DepositorMagni�cation 29000 DepositorImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 1.904 DepositorMinimum map value -0.909 DepositorAverage map value 0.001 DepositorMap value standard deviation 0.071 DepositorRecommended contour level 0.27 DepositorMap size (Å) 249.6, 249.6, 249.6 DepositorMap dimensions 300, 300, 300 DepositorMap angles (◦) 90.0, 90.0, 90.0 DepositorPixel spacing (Å) 0.832, 0.832, 0.832 Depositor

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#experimental_info


5 Model quality iO

5.1 Standard geometry iO

Bond lengths and bond angles in the following residue types are not validated in this section:PEF

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 anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).

Mol ChainBond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >5

1 A 0.25 0/1126 0.47 0/15311 B 0.25 0/1081 0.43 0/14701 C 0.25 0/1047 0.47 0/14291 D 0.25 0/1113 0.43 0/15121 E 0.25 0/1130 0.45 0/15371 F 0.25 0/1042 0.47 0/14222 G 0.26 0/1964 0.45 0/26692 H 0.26 0/1956 0.44 0/26583 I 0.25 0/2036 0.43 0/27643 J 0.25 0/2036 0.43 0/27644 K 0.26 0/743 0.44 0/10084 L 0.26 0/743 0.44 0/1008All All 0.25 0/16017 0.44 0/21772

There are no bond length outliers.

There are no bond angle outliers.

There are no chirality outliers.

There are no planarity outliers.

5.2 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 the chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashes withinthe asymmetric unit, whereas Symm-Clashes lists symmetry related clashes.

Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 A 1108 0 1133 22 0


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

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

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



Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 B 1063 0 1082 21 01 C 1033 0 973 14 01 D 1096 0 1120 11 01 E 1112 0 1138 16 01 F 1028 0 971 21 02 G 1926 0 2029 46 02 H 1918 0 2023 37 03 I 1996 0 2039 30 03 J 1996 0 2039 32 04 K 734 0 755 20 04 L 734 0 755 21 05 M 821 0 166 22 05 N 780 0 158 29 06 G 88 0 134 9 0All All 17433 0 16515 298 0

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 9.

All (298) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2Interatomicdistance (Å)

Clashoverlap (Å)

1:F:53:LYS:CD 2:G:191:ASN:HD22 1.61 1.131:F:53:LYS:HD3 2:G:191:ASN:ND2 1.68 1.071:F:53:LYS:CD 2:G:191:ASN:ND2 2.30 0.911:F:53:LYS:CG 2:G:191:ASN:HD22 1.84 0.892:G:89:MET:HG3 2:G:193:VAL:HG21 1.53 0.872:H:93:LEU:HD21 2:H:193:VAL:HB 1.55 0.851:F:53:LYS:CG 2:G:191:ASN:ND2 2.44 0.801:A:55:ARG:HD3 2:G:195:TRP:HZ3 1.49 0.762:H:93:LEU:HD11 2:H:193:VAL:CG1 2.16 0.761:A:55:ARG:HE 2:G:195:TRP:HE3 1.31 0.761:A:43:TYR:HB2 1:A:133:THR:HG22 1.68 0.752:H:93:LEU:HD11 2:H:193:VAL:HG11 1.73 0.711:D:142:VAL:HG21 1:E:102:ARG:HD3 1.72 0.714:K:44:LEU:HD12 4:K:77:VAL:HG22 1.74 0.701:E:69:ALA:HB3 1:E:83:THR:HG23 1.75 0.695:N:77:UNK:O 5:N:81:UNK:N 2.24 0.69

1:A:55:ARG:HD3 2:G:195:TRP:CZ3 2.27 0.692:G:126:THR:O 2:G:126:THR:HG22 1.93 0.694:L:44:LEU:HD12 4:L:77:VAL:HG22 1.74 0.69





Clashoverlap (Å)

1:C:69:ALA:HB3 1:C:83:THR:HG23 1.76 0.685:M:66:UNK:O 5:M:70:UNK:N 2.27 0.684:L:6:SER:HG 4:L:17:SER:HG 1.43 0.66

2:G:58:ILE:HD12 2:H:240:VAL:HG13 1.77 0.664:K:6:SER:HG 4:K:17:SER:HG 1.41 0.661:F:53:LYS:HG2 2:G:191:ASN:HD22 1.58 0.65

2:G:240:VAL:HG13 2:H:58:ILE:HD12 1.78 0.652:H:114:SER:HB2 2:H:235:THR:HG23 1.77 0.652:G:70:LEU:HD11 2:G:99:LEU:HD12 1.79 0.641:F:53:LYS:HG2 2:G:191:ASN:ND2 2.13 0.645:N:73:UNK:O 5:N:77:UNK:N 2.30 0.641:B:88:GLN:NE2 1:B:91:ASN:OD1 2.31 0.642:G:22:ARG:NH1 2:G:223:ASP:OD2 2.31 0.642:G:114:SER:HB2 2:G:235:THR:HG23 1.79 0.632:H:70:LEU:HD11 2:H:99:LEU:HD12 1.78 0.633:J:22:CYS:HB3 3:J:221:LYS:HE3 1.80 0.635:N:130:UNK:O 5:N:134:UNK:N 2.32 0.635:M:74:UNK:O 5:M:78:UNK:N 2.33 0.625:M:99:UNK:O 5:M:103:UNK:N 2.33 0.621:F:37:GLU:OE2 1:F:89:ARG:NH1 2.33 0.623:I:22:CYS:HB3 3:I:221:LYS:HE3 1.80 0.621:F:129:LYS:N 1:F:132:ASP:OD2 2.31 0.625:N:62:UNK:O 5:N:66:UNK:N 2.33 0.625:N:84:UNK:O 5:N:88:UNK:N 2.33 0.614:K:85:ALA:HB1 4:K:90:LEU:HD12 1.82 0.615:N:30:UNK:O 5:N:34:UNK:N 2.33 0.61

2:G:232:SER:HB3 2:H:118:ALA:HB1 1.81 0.614:L:85:ALA:HB1 4:L:90:LEU:HD12 1.82 0.615:M:59:UNK:O 5:M:63:UNK:N 2.34 0.611:B:49:ILE:HD13 1:B:71:ILE:HG21 1.83 0.601:B:103:THR:HG22 1:B:110:GLN:HG2 1.82 0.605:N:81:UNK:O 5:N:85:UNK:N 2.34 0.60

2:H:227:THR:HG23 2:H:230:GLY:H 1.66 0.595:M:63:UNK:O 5:M:67:UNK:N 2.34 0.592:G:36:GLU:HA 2:G:141:ARG:HH12 1.67 0.595:M:77:UNK:O 5:M:81:UNK:N 2.34 0.591:A:71:ILE:HG12 1:A:82:VAL:HG12 1.85 0.584:L:7:TRP:HB2 4:L:14:LEU:HD11 1.85 0.585:M:69:UNK:O 5:M:73:UNK:N 2.36 0.581:B:53:LYS:NZ 2:H:75:TYR:OH 2.37 0.582:G:73:GLN:NE2 2:H:98:GLU:OE1 2.37 0.58





Clashoverlap (Å)

4:K:39:ILE:O 4:K:70:ASN:ND2 2.37 0.585:N:45:UNK:O 5:N:49:UNK:N 2.36 0.584:K:7:TRP:HB2 4:K:14:LEU:HD11 1.85 0.584:L:39:ILE:O 4:L:70:ASN:ND2 2.37 0.58

5:M:134:UNK:O 5:M:138:UNK:N 2.36 0.585:N:87:UNK:O 5:N:91:UNK:N 2.37 0.58

4:K:62:ILE:HD11 4:K:74:LEU:HD21 1.87 0.571:E:8:ILE:O 1:E:12:ILE:HG13 2.04 0.57

1:A:41:THR:HG22 1:A:85:GLU:HG2 1.86 0.571:E:49:ILE:HD13 1:E:71:ILE:HG21 1.87 0.575:N:86:UNK:O 5:N:90:UNK:N 2.38 0.574:L:62:ILE:HD11 4:L:74:LEU:HD21 1.87 0.575:N:70:UNK:O 5:N:74:UNK:N 2.38 0.561:D:69:ALA:HB3 1:D:83:THR:HG23 1.86 0.561:E:71:ILE:HG12 1:E:82:VAL:HG23 1.87 0.561:B:69:ALA:HB3 1:B:83:THR:HG23 1.87 0.562:G:89:MET:HG3 2:G:193:VAL:CG2 2.31 0.555:M:25:UNK:O 5:M:29:UNK:N 2.39 0.552:G:94:SER:HA 6:G:302:PEF:H351 1.87 0.555:M:62:UNK:O 5:M:66:UNK:N 2.39 0.55

1:B:10:VAL:HG11 2:G:25:LEU:HG 1.88 0.551:C:36:THR:OG1 1:C:37:GLU:N 2.40 0.555:N:105:UNK:O 5:N:109:UNK:N 2.40 0.552:H:93:LEU:CD1 2:H:193:VAL:HG11 2.36 0.551:B:55:ARG:NH2 2:H:177:TRP:O 2.40 0.553:I:232:LEU:O 3:I:241:ARG:NH2 2.38 0.55

1:D:49:ILE:HD13 1:D:71:ILE:HG21 1.89 0.552:G:155:LEU:HB3 2:G:210:ALA:HB2 1.89 0.552:H:155:LEU:HB3 2:H:210:ALA:HB2 1.89 0.553:J:95:ALA:O 3:J:157:ARG:NH1 2.40 0.54

3:J:51:LEU:HD22 3:J:167:MET:HB3 1.90 0.543:I:95:ALA:O 3:I:157:ARG:NH1 2.41 0.54

3:I:87:MET:HG2 3:I:165:LEU:HD23 1.89 0.544:L:66:LYS:NZ 4:L:93:ASP:O 2.41 0.541:A:55:ARG:NE 2:G:195:TRP:HE3 2.03 0.542:H:36:GLU:O 2:H:40:HIS:ND1 2.41 0.543:J:232:LEU:O 3:J:241:ARG:NH2 2.38 0.545:M:80:UNK:O 5:M:84:UNK:N 2.41 0.541:F:36:THR:OG1 1:F:37:GLU:N 2.41 0.541:E:103:THR:HG22 1:E:110:GLN:HG2 1.90 0.531:B:95:ASP:OD2 1:B:126:ALA:N 2.41 0.53





Clashoverlap (Å)

1:A:49:ILE:HD13 1:A:71:ILE:HG21 1.90 0.534:K:66:LYS:NZ 4:K:93:ASP:O 2.41 0.53

1:A:84:LEU:HD13 1:A:86:ILE:HG13 1.90 0.533:I:51:LEU:HD22 3:I:167:MET:HB3 1.90 0.535:N:97:UNK:O 5:N:101:UNK:N 2.42 0.53

3:I:151:ARG:NH2 3:I:171:PRO:O 2.41 0.533:J:87:MET:HG2 3:J:165:LEU:HD23 1.89 0.535:M:81:UNK:O 5:M:85:UNK:N 2.42 0.535:N:108:UNK:O 5:N:112:UNK:N 2.42 0.525:N:41:UNK:O 5:N:45:UNK:N 2.41 0.524:L:6:SER:OG 4:L:17:SER:OG 2.22 0.52

3:I:170:GLU:HG3 3:I:202:SER:HA 1.92 0.523:J:151:ARG:NH2 3:J:171:PRO:O 2.41 0.521:D:28:ALA:HA 2:H:194:ASP:CB 2.40 0.523:J:131:ALA:HB2 4:L:88:TYR:CD1 2.45 0.522:H:36:GLU:OE2 2:H:149:TRP:NE1 2.38 0.511:C:95:ASP:OD1 1:C:95:ASP:N 2.42 0.511:F:53:LYS:HB3 2:G:191:ASN:HD21 1.75 0.511:B:120:ASP:HB2 1:B:123:LEU:HB2 1.92 0.515:N:101:UNK:O 5:N:105:UNK:N 2.43 0.514:K:26:LEU:O 4:K:30:GLU:HG3 2.11 0.51

3:J:170:GLU:HG3 3:J:202:SER:HA 1.92 0.515:N:99:UNK:O 5:N:103:UNK:N 2.44 0.511:A:27:LYS:O 2:G:189:MET:HE3 2.11 0.51

1:E:29:ALA:HB2 2:H:256:LEU:HD23 1.92 0.515:M:5:UNK:O 5:M:9:UNK:N 2.44 0.51

1:C:52:LEU:HD21 1:C:68:VAL:HG21 1.93 0.511:E:38:PRO:HB2 1:E:88:GLN:H 1.76 0.501:F:53:LYS:CE 2:G:191:ASN:HD22 2.21 0.504:L:26:LEU:O 4:L:30:GLU:HG3 2.11 0.50

3:I:53:LEU:HD23 3:I:58:ILE:HG13 1.94 0.505:N:98:UNK:O 5:N:102:UNK:N 2.45 0.505:N:126:UNK:O 5:N:130:UNK:N 2.45 0.50

6:G:302:PEF:H221 2:H:90:LEU:HD11 1.93 0.503:I:131:ALA:HB2 4:K:88:TYR:CD1 2.46 0.501:F:101:ILE:HG12 1:F:112:LEU:HD23 1.93 0.494:K:23:ASP:OD1 4:K:24:VAL:HG13 2.12 0.491:B:132:ASP:OD1 1:B:133:THR:N 2.45 0.494:L:95:LEU:O 4:L:97:ARG:NH1 2.46 0.49

1:A:42:LEU:HB2 1:A:84:LEU:HD11 1.92 0.491:A:102:ARG:HG2 1:F:144:GLU:HG3 1.94 0.49





Clashoverlap (Å)

3:J:53:LEU:HD23 3:J:58:ILE:HG13 1.94 0.494:L:23:ASP:OD1 4:L:24:VAL:HG13 2.12 0.491:C:94:PRO:HG3 1:C:119:GLU:HG3 1.95 0.492:H:119:GLU:OE2 2:H:147:ARG:NH2 2.35 0.494:K:95:LEU:O 4:K:97:ARG:NH1 2.46 0.49

3:I:106:VAL:HG21 3:I:129:LEU:HD21 1.95 0.491:E:77:THR:HG23 1:E:79:LEU:H 1.78 0.481:F:49:ILE:HD13 1:F:71:ILE:HG21 1.93 0.483:I:40:MET:HE1 3:I:209:LEU:HD21 1.95 0.485:N:52:UNK:O 5:N:56:UNK:N 2.45 0.48

1:D:132:ASP:OD1 1:D:133:THR:N 2.45 0.485:N:95:UNK:O 5:N:99:UNK:N 2.46 0.48

1:A:60:ILE:HG13 1:A:65:VAL:HG21 1.95 0.481:E:37:GLU:HA 1:E:39:THR:HG23 1.95 0.483:I:128:LYS:HE3 3:I:160:ALA:HA 1.95 0.483:J:128:LYS:HE3 3:J:160:ALA:HA 1.95 0.481:B:49:ILE:HD12 1:B:71:ILE:HD13 1.96 0.481:D:73:LEU:HG 1:E:63:VAL:HG11 1.95 0.482:G:126:THR:O 2:G:126:THR:CG2 2.61 0.48

1:A:146:LEU:HD11 1:F:147:ILE:HD13 1.96 0.481:D:5:LYS:NZ 2:H:49:TYR:OH 2.47 0.471:B:38:PRO:O 1:B:88:GLN:HB2 2.14 0.475:N:42:UNK:O 5:N:46:UNK:N 2.47 0.47

3:J:106:VAL:HG21 3:J:129:LEU:HD21 1.95 0.473:I:130:GLU:OE2 3:J:255:ARG:NH2 2.48 0.473:J:146:SER:OG 3:J:147:GLY:N 2.48 0.474:L:55:LEU:O 4:L:59:LEU:HG 2.15 0.47

4:K:62:ILE:HD13 4:K:96:PRO:HD2 1.97 0.471:E:132:ASP:OD1 1:E:133:THR:N 2.44 0.472:G:100:GLY:HA2 2:G:162:PHE:CE2 2.50 0.475:M:60:UNK:O 5:M:64:UNK:N 2.48 0.47

6:G:302:PEF:H362 6:G:302:PEF:H332 1.73 0.461:C:144:GLU:HG3 1:D:102:ARG:HG2 1.98 0.462:H:100:GLY:HA2 2:H:162:PHE:CE2 2.51 0.463:I:242:GLN:HE22 3:I:252:VAL:HB 1.81 0.465:M:102:UNK:O 5:M:106:UNK:N 2.48 0.461:F:7:GLU:O 2:H:10:GLY:HA3 2.16 0.465:N:67:UNK:O 5:N:71:UNK:N 2.49 0.46

1:C:58:VAL:HG22 1:C:112:LEU:HB2 1.97 0.461:C:49:ILE:HD13 1:C:71:ILE:HG21 1.98 0.461:F:142:VAL:HG23 1:F:145:ASP:HB2 1.96 0.46





Clashoverlap (Å)

4:L:62:ILE:HD13 4:L:96:PRO:HD2 1.97 0.461:C:46:PHE:HZ 1:C:99:LEU:HD23 1.81 0.46

2:G:93:LEU:HD22 2:G:198:ASP:OD2 2.15 0.461:E:49:ILE:HD12 1:E:71:ILE:HD13 1.97 0.466:G:301:PEF:H201 6:G:301:PEF:H172 1.72 0.462:G:66:ILE:CD1 2:G:103:VAL:HG11 2.46 0.463:J:40:MET:HE1 3:J:209:LEU:HD21 1.98 0.461:C:130:ASP:OD1 1:C:131:GLY:N 2.48 0.462:G:90:LEU:HD12 6:G:302:PEF:H312 1.98 0.462:G:36:GLU:HG2 2:G:37:PHE:HD1 1.80 0.463:I:146:SER:OG 3:I:147:GLY:N 2.48 0.464:K:21:ASP:OD1 4:K:21:ASP:N 2.49 0.461:B:7:GLU:HA 1:B:10:VAL:HG12 1.96 0.45

2:G:119:GLU:OE2 2:G:147:ARG:NH2 2.34 0.454:K:55:LEU:O 4:K:59:LEU:HG 2.15 0.454:L:21:ASP:OD1 4:L:21:ASP:N 2.49 0.451:A:152:TYR:HE1 1:B:149:GLN:HE22 1.62 0.451:D:2:GLN:OE1 1:D:2:GLN:N 2.49 0.451:A:27:LYS:HB3 2:G:189:MET:CE 2.47 0.45

1:E:107:LEU:HD11 6:G:301:PEF:H212 1.99 0.451:B:7:GLU:OE2 2:G:18:ARG:HA 2.17 0.453:I:255:ARG:NH2 3:J:130:GLU:OE2 2.49 0.452:H:55:SER:O 2:H:55:SER:OG 2.33 0.455:N:91:UNK:O 5:N:95:UNK:N 2.49 0.45

3:J:242:GLN:HE22 3:J:252:VAL:HB 1.81 0.451:E:25:CYS:HB3 2:H:256:LEU:HD21 1.98 0.453:J:39:ILE:HB 3:J:201:VAL:HG22 1.99 0.451:A:47:ASP:N 1:A:47:ASP:OD1 2.49 0.451:B:119:GLU:N 1:B:119:GLU:OE1 2.46 0.451:C:129:LYS:N 1:C:132:ASP:OD2 2.50 0.45

1:B:39:THR:HG22 1:B:87:GLU:HA 1.99 0.445:M:128:UNK:O 5:M:132:UNK:N 2.50 0.443:I:39:ILE:HB 3:I:201:VAL:HG22 1.99 0.444:K:6:SER:OG 4:K:17:SER:OG 2.22 0.44

1:D:36:THR:OG1 1:D:37:GLU:N 2.51 0.443:I:202:SER:OG 3:I:203:HIS:N 2.51 0.443:I:135:ARG:NH1 3:J:260:ASP:O 2.49 0.444:L:80:LYS:HB2 4:L:80:LYS:HE3 1.79 0.445:M:133:UNK:O 5:M:137:UNK:N 2.51 0.443:J:202:SER:OG 3:J:203:HIS:N 2.51 0.432:H:108:PHE:O 2:H:113:GLY:N 2.51 0.43





Clashoverlap (Å)

2:H:225:ILE:HG22 2:H:227:THR:HG22 2.00 0.433:I:101:ASN:O 3:I:105:ASN:ND2 2.45 0.433:I:260:ASP:O 3:J:135:ARG:NH1 2.49 0.435:N:96:UNK:O 5:N:100:UNK:N 2.52 0.43

2:G:168:TRP:CH2 2:G:172:LEU:HD11 2.54 0.432:G:36:GLU:HA 2:G:141:ARG:NH1 2.33 0.436:G:302:PEF:H402 2:H:99:LEU:HD11 2.00 0.432:H:145:SER:OG 2:H:146:PRO:HD3 2.19 0.431:C:101:ILE:HG12 1:C:112:LEU:HD23 2.00 0.432:H:168:TRP:CH2 2:H:172:LEU:HD11 2.54 0.435:M:88:UNK:O 5:M:92:UNK:N 2.51 0.43

2:H:135:MET:HE1 3:J:157:ARG:HH21 1.83 0.433:I:181:GLY:HA2 3:I:184:VAL:HG12 2.01 0.435:M:2:UNK:O 5:M:6:UNK:N 2.52 0.434:K:21:ASP:HA 4:K:51:ASP:OD1 2.19 0.434:L:23:ASP:OD1 4:L:24:VAL:N 2.52 0.435:N:80:UNK:O 5:N:84:UNK:N 2.52 0.43

3:J:181:GLY:HA2 3:J:184:VAL:HG12 2.01 0.422:G:113:GLY:O 2:G:217:SER:HB2 2.19 0.425:M:142:UNK:O 5:M:146:UNK:N 2.52 0.421:A:88:GLN:HE21 1:A:91:ASN:ND2 2.17 0.421:D:27:LYS:HA 1:D:27:LYS:HD3 1.87 0.424:K:82:TYR:OH 4:K:97:ARG:O 2.29 0.424:L:21:ASP:HA 4:L:51:ASP:OD1 2.19 0.421:E:129:LYS:HB3 1:E:129:LYS:HE2 1.84 0.423:J:92:GLN:O 3:J:151:ARG:NE 2.48 0.42

4:L:55:LEU:HD21 4:L:81:VAL:HG13 2.02 0.424:K:23:ASP:OD1 4:K:24:VAL:N 2.52 0.421:F:38:PRO:O 1:F:88:GLN:HB2 2.18 0.42

2:H:36:GLU:HB2 2:H:141:ARG:HH12 1.84 0.422:G:36:GLU:HG2 2:G:37:PHE:CD1 2.54 0.425:M:127:UNK:O 5:M:131:UNK:N 2.53 0.425:N:33:UNK:O 5:N:37:UNK:N 2.53 0.42

6:G:302:PEF:H361 6:G:302:PEF:H392 1.58 0.423:I:39:ILE:HG21 3:I:50:LEU:HD23 2.02 0.425:N:78:UNK:O 5:N:82:UNK:N 2.53 0.423:J:13:ASP:H 3:J:28:SER:HB3 1.85 0.41

1:A:76:LYS:HD2 1:A:76:LYS:HA 1.86 0.411:B:142:VAL:HG23 1:B:145:ASP:HB2 2.03 0.413:J:131:ALA:HB2 4:L:88:TYR:HD1 1.85 0.411:A:88:GLN:HE21 1:A:91:ASN:HD21 1.67 0.41





Clashoverlap (Å)

1:C:48:ASN:N 1:C:139:SER:OG 2.48 0.413:J:39:ILE:HG21 3:J:50:LEU:HD23 2.02 0.414:K:80:LYS:HE3 4:K:80:LYS:HB2 1.79 0.413:I:45:ILE:HD13 3:I:218:LEU:HD23 2.02 0.413:I:49:THR:HG23 3:I:58:ILE:HD11 2.03 0.413:I:67:PHE:HB2 3:I:72:ILE:HD11 2.02 0.412:H:139:PRO:O 2:H:143:VAL:HG12 2.20 0.413:I:100:MET:HB2 3:I:104:ASP:HB2 2.02 0.413:J:45:ILE:HD13 3:J:218:LEU:HD23 2.02 0.415:N:1:UNK:O 5:N:5:UNK:N 2.53 0.41

1:A:40:TYR:CE2 1:A:42:LEU:HD11 2.55 0.413:I:13:ASP:H 3:I:28:SER:HB3 1.85 0.41

3:J:137:ALA:HA 3:J:140:LEU:HD13 2.02 0.411:F:53:LYS:CB 2:G:191:ASN:ND2 2.84 0.412:H:38:ARG:HA 2:H:38:ARG:HD3 1.82 0.413:J:49:THR:HG23 3:J:58:ILE:HD11 2.03 0.414:K:55:LEU:HD21 4:K:81:VAL:HG13 2.02 0.412:G:81:TYR:OH 6:G:301:PEF:H121 2.21 0.412:G:98:GLU:OE2 2:G:254:THR:OG1 2.38 0.413:J:67:PHE:HB2 3:J:72:ILE:HD11 2.02 0.41

1:A:106:LEU:HD23 1:F:106:LEU:HD22 2.03 0.401:B:112:LEU:HD23 1:B:112:LEU:HA 1.91 0.401:B:95:ASP:HA 1:B:128:LEU:HD21 2.03 0.401:B:107:LEU:O 2:H:82:SER:HB3 2.21 0.405:M:156:UNK:O 5:M:160:UNK:N 2.54 0.40

1:C:142:VAL:HG23 1:C:145:ASP:OD1 2.22 0.402:G:99:LEU:HD23 2:G:99:LEU:HA 1.87 0.402:H:205:LYS:HE3 2:H:257:MET:HE1 2.02 0.403:J:100:MET:HB2 3:J:104:ASP:HB2 2.02 0.402:G:244:LEU:HD21 2:H:58:ILE:HG13 2.03 0.403:I:137:ALA:HA 3:I:140:LEU:HD13 2.02 0.403:J:85:LYS:HE2 3:J:113:HIS:ND1 2.37 0.40

3:I:266:LEU:HD13 4:L:63:ASP:HB2 2.04 0.40

There are no symmetry-related clashes.


5.3 Torsion angles iO

5.3.1 Protein backbone iO

In the following table, the Percentiles column shows the percent Ramachandran outliers of thechain as a percentile score with respect to all PDB entries followed by that with respect to all EMentries.

The Analysed column shows the number of residues for which the backbone conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 A 140/201 (70%) 136 (97%) 4 (3%) 0 100 100

1 B 134/201 (67%) 129 (96%) 5 (4%) 0 100 100

1 C 140/201 (70%) 137 (98%) 3 (2%) 0 100 100

1 D 137/201 (68%) 134 (98%) 3 (2%) 0 100 100

1 E 141/201 (70%) 131 (93%) 10 (7%) 0 100 100

1 F 139/201 (69%) 132 (95%) 7 (5%) 0 100 100

2 G 254/260 (98%) 248 (98%) 6 (2%) 0 100 100

2 H 253/260 (97%) 242 (96%) 11 (4%) 0 100 100

3 I 261/269 (97%) 253 (97%) 8 (3%) 0 100 100

3 J 261/269 (97%) 253 (97%) 8 (3%) 0 100 100

4 K 93/97 (96%) 90 (97%) 3 (3%) 0 100 100

4 L 93/97 (96%) 90 (97%) 3 (3%) 0 100 100

All All 2046/2458 (83%) 1975 (96%) 71 (4%) 0 100 100

There are no Ramachandran outliers to report.

5.3.2 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 EMentries.

The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles

1 A 121/167 (72%) 121 (100%) 0 100 100

1 B 116/167 (70%) 116 (100%) 0 100 100Continued on next page...

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

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

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



Mol Chain Analysed Rotameric Outliers Percentiles

1 C 100/167 (60%) 100 (100%) 0 100 100

1 D 119/167 (71%) 119 (100%) 0 100 100

1 E 121/167 (72%) 121 (100%) 0 100 100

1 F 100/167 (60%) 100 (100%) 0 100 100

2 G 205/209 (98%) 204 (100%) 1 (0%) 88 94

2 H 204/209 (98%) 204 (100%) 0 100 100

3 I 215/220 (98%) 215 (100%) 0 100 100

3 J 215/220 (98%) 215 (100%) 0 100 100

4 K 82/84 (98%) 82 (100%) 0 100 100

4 L 82/84 (98%) 82 (100%) 0 100 100

All All 1680/2028 (83%) 1679 (100%) 1 (0%) 93 97

All (1) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type2 G 197 MET

Some sidechains can be �ipped to improve hydrogen bonding and reduce clashes. All (12) suchsidechains are listed below:

Mol Chain Res Type1 A 2 GLN1 A 88 GLN1 B 88 GLN1 B 91 ASN1 B 149 GLN1 C 135 GLN1 D 2 GLN2 G 191 ASN3 I 191 ASN3 I 226 HIS3 J 191 ASN3 J 226 HIS

5.3.3 RNA iO

There are no RNA molecules in this entry.

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


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

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

5.5 Carbohydrates iO

There are no monosaccharides in this entry.

5.6 Ligand geometry iO

2 ligands are modelled in this entry.

In the following table, the Counts columns list the number of bonds (or angles) for which Mogulstatistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are de�ned in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bondlength (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

Mol Type Chain Res LinkBond lengths Bond angles

Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

6 PEF G 302 - 43,43,46 1.06 2 (4%) 47,48,51 0.93 2 (4%)

6 PEF G 301 - 43,43,46 1.06 2 (4%) 47,48,51 0.91 2 (4%)

In the following table, the Chirals column lists the number of chiral outliers, the number of chiralcenters analysed, the number of these observed in the model and the number de�ned in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.'-' means no outliers of that kind were identi�ed.

Mol Type Chain Res Link Chirals Torsions Rings6 PEF G 302 - - 27/45/45/50 -

6 PEF G 301 - - 24/45/45/50 -

All (4) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)6 G 302 PEF O2-C10 3.68 1.44 1.346 G 301 PEF O2-C10 3.62 1.44 1.346 G 302 PEF O3-C30 2.67 1.41 1.336 G 301 PEF O3-C30 2.67 1.41 1.33

All (4) bond angle outliers are listed below:

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




Mol Chain Res Type Atoms Z Observed(o) Ideal(o)6 G 302 PEF O2-C10-C11 3.88 119.87 111.506 G 301 PEF O2-C10-C11 3.84 119.77 111.506 G 301 PEF O3-C30-C31 2.67 120.29 111.916 G 302 PEF O3-C30-C31 2.64 120.20 111.91

There are no chirality outliers.

All (51) torsion outliers are listed below:

Mol Chain Res Type Atoms6 G 302 PEF C31-C30-O3-C36 G 302 PEF O5-C30-O3-C36 G 301 PEF C31-C30-O3-C36 G 301 PEF O5-C30-O3-C36 G 301 PEF C34-C35-C36-C376 G 302 PEF C36-C37-C38-C396 G 301 PEF C17-C18-C19-C206 G 301 PEF C10-C11-C12-C136 G 302 PEF C11-C12-C13-C146 G 301 PEF C39-C40-C41-C426 G 302 PEF C21-C22-C23-C246 G 302 PEF C39-C40-C41-C426 G 302 PEF C12-C13-C14-C156 G 301 PEF C38-C39-C40-C416 G 302 PEF C31-C32-C33-C346 G 301 PEF C12-C13-C14-C156 G 301 PEF C21-C22-C23-C246 G 302 PEF C34-C35-C36-C376 G 301 PEF C42-C43-C44-C456 G 301 PEF C11-C10-O2-C26 G 302 PEF C42-C43-C44-C456 G 301 PEF C31-C32-C33-C346 G 302 PEF C35-C36-C37-C386 G 302 PEF O3P-C1-C2-O26 G 302 PEF C22-C23-C24-C256 G 301 PEF O2-C2-C3-O36 G 301 PEF C22-C23-C24-C256 G 302 PEF C10-C11-C12-C136 G 301 PEF C35-C36-C37-C386 G 302 PEF C38-C39-C40-C416 G 301 PEF O4-C10-O2-C26 G 301 PEF C36-C37-C38-C396 G 301 PEF C1-C2-C3-O36 G 302 PEF O3P-C1-C2-C3




Mol Chain Res Type Atoms6 G 302 PEF C16-C17-C18-C196 G 301 PEF C14-C15-C16-C176 G 302 PEF C15-C16-C17-C186 G 302 PEF O2-C2-C3-O36 G 302 PEF C14-C15-C16-C176 G 302 PEF C13-C14-C15-C166 G 301 PEF C40-C41-C42-C436 G 301 PEF O3P-C1-C2-O26 G 302 PEF C30-C31-C32-C336 G 302 PEF C32-C33-C34-C356 G 302 PEF C1-C2-C3-O36 G 302 PEF C33-C34-C35-C366 G 301 PEF O3P-C1-C2-C36 G 301 PEF O2-C10-C11-C126 G 302 PEF O2-C10-C11-C126 G 301 PEF O4-C10-C11-C126 G 302 PEF O4-C10-C11-C12

There are no ring outliers.

2 monomers are involved in 9 short contacts:

Mol Chain Res Type Clashes Symm-Clashes6 G 302 PEF 6 06 G 301 PEF 3 0

The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. Inaddition, ligands with molecular weight > 250 and outliers as shown on the validation Tables willalso be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles iswithin 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier.Any bond that is central to one or more torsion angles identi�ed as an outlier by Mogul will behighlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ringin question and similar rings identi�ed by Mogul is calculated over all ring torsion angles. If theaverage RMSD is greater than 60 degrees and the minimal RMSD between the ring in question andany Mogul-identi�ed rings is also greater than 60 degrees, then that ring is considered an outlier.The outliers are highlighted in purple. The color gray indicates Mogul did not �nd su�cientequivalents in the CSD to analyse the geometry.


Ligand PEF G 302

Bond lengths Bond angles

Torsions Rings

Ligand PEF G 301

Bond lengths Bond angles

Torsions Rings

5.7 Other polymers iO

There are no such residues in this entry.

5.8 Polymer linkage issues iO

There are no chain breaks in this entry.


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


6 Map visualisation iO

This section contains visualisations of the EMDB entry EMD-22116. These are intended to permitvisual inspection of the internal detail of the map and identi�cation of artifacts.

6.1 Orthogonal projections iO

X Y Z

The images above show the map projected in three orthogonal projections, in greyscale.

6.2 Central slices iO

X Y Z

The images above show central slices of the map in three orthogonal directions, in greyscale.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_visualisation

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#orthogonal_projections

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#central_slices


6.3 Largest variance slices iO

X Index: 162 Y Index: 144 Z Index: 198

The images above show the highest variance slices of the map in three orthogonal directions, ingreyscale.

6.4 Orthogonal surface views iO

X Y Z

The images above show the 3D surface view of the map at the recommended contour level 0.27.This in conjunction with the slice images can indicate whether an appropriate contour level hasbeen selected.

6.5 Mask visualisation iO

This section was not generated. No masks were provided.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#largest_variance_slices

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#orthogonal_views

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#masks


7 Map analysis iO

This section contains the results of statistical analysis of the map.

7.1 Map-value distribution iO

The map-value distribution is plotted in 128 intervals along the x-axis. The y-axis is logarithmic.A spike in this graph at zero usually indicates that the volume has been masked.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_analysis

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_value_distribution


7.2 Volume estimate iO

The volume at the recommended contour level is 132 nm3; this corresponds to an approximatemass of 120 kDa.

The volume estimate graph shows how the enclosed volume varies with the contour level. Therecommended contour level is shown as a vertical line and the intersection between the line andthe curve gives the volume of the enclosed surface at the given level.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#volume_estimate


7.3 Rotationally averaged power spectrum iO

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#raps


8 Fourier-Shell correlation iO

This section was not generated. No FSC curve or half maps provided.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#fsc_validation


9 Map-model �t iO

This section contains information regarding the �t between EMDB map EMD-22116 and PDBmodel 6XBD. Per-residue inclusion information can be found in section 3 on page 9.

9.1 Map-model overlay iO

X Y Z

The images above show the 3D surface view of the map at the recommended contour level 0.27 at50% transparency in yellow overlaid with a ribbon representation of the model coloured in blue.These images allow for the visual assessment of the quality of �t between the atomic model andthe map.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_fit

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_overlay


9.2 Atom inclusion iO

At the recommended contour level, 88% of all backbone atoms, 84% of all non-hydrogen atoms,are inside the map.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#atom_inclusion_by_contour

full wwpdb em model validation report i · 2020-06-22 · full wwpdb em model validation report i...

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