Full wwPDB EM Validation Report O i...N.; Aebersold, R.; Ban, N. Deposited on : 2014-09-25...

Full wwPDB EM Validation Report iO

Dec 6, 2020 � 01:06 am GMT

PDB ID : 4V1AEMDB ID : EMD-2787

Title : Structure of the large subunit of the mammalian mitoribosome, part 2 of 2Authors : Greber, B.J.; Boehringer, D.; Leibundgut, M.; Bieri, P.; Leitner, A.; Schmitz,

N.; Aebersold, R.; Ban, N.Deposited on : 2014-09-25Resolution : 3.40 Å(reported)

This is a Full wwPDB EM 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.dev61MolProbity : 4.02b-467

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) : 2.15.1

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

Full wwPDB EM Validation Report EMD-2787, 4V1A

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 3.40 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 �tto the map. The red, orange, yellow and green segments of the bar indicate the fraction of residuesthat contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. A greysegment 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


Continued from previous page...

Mol Chain Length Quality of chain

9 i 312

10 j 279

11 k 212

12 l 166

13 m 159

14 n 128

15 o 124

16 p 112

17 q 138

18 t 102

19 u 205

20 v 222

21 w 433

22 x 196

23 z 47


2 Entry composition iO

There are 24 unique types of molecules in this entry. The entry contains 31917 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 MITORIBOSOMAL PROTEIN ML37, MRPL37.

Mol Chain Residues Atoms AltConf Trace

1 a 393Total C N O S3173 2040 556 565 12

0 0



2 b 354Total C N O S2952 1876 542 525 9

0 0



3 c 295Total C N O S2408 1541 410 441 16

0 0



4 d 99Total C N O S832 528 148 155 1

0 0



5 e 121Total C N O S968 626 167 172 3

0 0



6 f 108Total C N O S852 544 154 150 4

0 0

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




7 g 148Total C N O S1167 727 225 212 3

0 0



8 h 289Total C N O S2319 1486 399 426 8

0 0



9 i 242Total C N O S1979 1266 352 351 10

0 0



10 j 217Total C N O S1775 1137 311 321 6

0 0



11 k 131Total C N O S1050 671 178 196 5

0 0



12 l 133Total C N O S1097 709 192 194 2

0 0



13 m 109Total C N O S893 568 160 162 3

0 0




14 n 97Total C N O S837 539 166 128 4

0 0



15 o 94Total C N O S747 466 143 136 2

0 0



16 p 97Total C N O S742 459 143 134 6

0 0



17 q 37Total C N O336 214 69 53

0 0

Molecule 18 is a protein called MITORIBOSOMAL PROTEIN ML63, MRPL57, MRP63.


18 t 94Total C N O S780 485 168 126 1

0 0

Molecule 19 is a protein called MITORIBOSOMAL PROTEIN ML62, MRPL58, ICT1.


19 u 151Total C N O S1208 748 233 222 5

0 0

Molecule 20 is a protein called MITORIBOSOMAL PROTEIN ML64, MRPL59, CRIF1.


20 v 131Total C N O S1068 662 206 195 5

0 0

Molecule 21 is a protein called MITORIBOSOMAL PROTEIN ML65, MRPS30.



21 w 387Total C N O S3126 2011 548 555 12

0 0

Molecule 22 is a protein called MITORIBOSOMAL PROTEIN ML66, MRPS18A.


22 x 162Total C N O S1325 845 249 224 7

0 0

Molecule 23 is a protein called UNASSIGNED SECONDARY STRUCTURE ELEMENTS.


23 z 47Total C N O282 188 47 47

0 0

Molecule 24 is ZINC ION (three-letter code: ZN) (formula: Zn).

Mol Chain Residues Atoms AltConf

24 x 1Total Zn1 1

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: MITORIBOSOMAL PROTEIN ML37, MRPL37

Chain a:

MET

ALA

LEU

ALA

SER

GLY

PRO

ALA

ARG

ARG

ALA

LEU

ALA

ARG

PRO

GLY

ARG

LEU

GLY

PHE

GLY

GLY

CYS

GLY

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ARG

ARG

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A30

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K40

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N207

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E244�

T248

E254�

C268

N269

V270

N274

T277

V335

D348

E368�

K393�

V398

A422

VAL


Chain b:

MET

ALA

ALA

PRO

TRP

TRP

ARG

ALA

ALA

LEU

CYS

ALA

SER

ARG

ARG

TRP

ARG

GLY

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R27

D39

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G79

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S288

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Y380


Chain c:

MET

ALA

MET

GLY

ALA

TRP

GLY

LEU

ARG

LEU

TRP

ARG

ALA

VAL

PRO

ARG

GLY

GLU

ALA

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ALA

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ALA

S30

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L211

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C272

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T285

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S287�

N310

E322�

D323�

K324�

THR

LYS

PRO

THR

GLU

GLU

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ALA

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Chain d:

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


MET

ALA

ALA

ALA

ALA

LEU

GLY

ALA

ALA

SER

ARG

THR

LEU

ARG

PRO

ALA

SER

ARG

LEU

VAL

GLY

ALA

TRP

PRO

THR

GLN

THR

ARG

ASP

ALA

HIS

GLU

ARG

GLY

SER

LEU

PHE

SER

PHE

TRP

GLY

LEU

VAL

PRO

MET

ARG

ALA

GLU

PRO

LEU

ARG

LYS

LYS

LYS

LYS

VAL

ASP

PRO

LYS

LYS

ASP

GLN

ALA

ALA

LYS

ASP

ARG

LEU

LYS

LYS

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ARG

ARG

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P181

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ASP

TYR

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PRO

PRO

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ARG

TYR

GLN

ASP

ILE

THR

LYS

VAL

TYR

THR

GLN

VAL

GLU

PHE

LYS

LYS


Chain e:

MET

GLY

LEU

LEU

SER

GLY

ALA

ALA

ARG

ALA

LEU

VAL

ARG

GLY

A15

S19

D45

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G65

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�G79

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G105

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L112

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Q127

R135


Chain f:

MET

ALA

LEU

ALA

ALA

VAL

LYS

TRP

VAL

ILE

SER

SER

ARG

THR

ILE

LEU

LYS

HIS

LEU

PHE

PRO

ILE

GLN

ASN

SER

ALA

SER

TYR

CYS

VAL

CYS

HIS

LYS

SER

T35

�

N44

V59

S64

V65

D66

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X78

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H121

R122

R131

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Chain g:

MET

T2

T6

R9

V14

R21

R28

L33

S34

S39

R49

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C70

V94

S108

V112

I113

R114

I126

T138

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ASP

PRO

ALA

PRO

ALA

GLN

VAL

GLN

ALA

GLN


Chain h:

MET

ALA

SER

GLY

LEU

VAL

ARG

LEU

LEU

GLN

TRP

GLY

PRO

ARG

ARG

LEU

LEU

ALA

PRO

ALA

ALA

PRO

THR

LEU

ALA

PRO

PRO

VAL

ARG

GLY

A31

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L88

I98

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L148

C167

R171

S181

L191

R192

T211

R216

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M231

W232

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T288

L301

K318�

P319�

LYS

GLU

HIS

VAL

ARG

ALA

GLU

LYS

THR

ILE

THR

ALA

SER



Chain i:

MET

ALA

ALA

PRO

VAL

THR

ARG

GLY

LEU

SER

CYS

LEU

PRO

ARG

VAL

LEU

GLY

TRP

TRP

SER

ARG

GLN

PRO

VAL

LEU

VAL

THR

GLN

SER

THR

ALA

VAL

VAL

PRO

VAL

ARG

THR

LYS

LYS

ARG

PHE

THR

PRO

PRO

THR

TYR

GLN

PRO

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GLU

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A79

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GLY

GLU

VAL

HIS

LYS

PRO

GLN

PRO

ALA

ARG

ARG

ARG

ASN

ASP

SER


Chain j:

MET

ALA

ALA

PRO

VAL

ARG

ARG

THR

MET

LEU

ARG

VAL

VAL

ARG

GLY

TRP

ARG

ARG

PHE

GLU

GLY

PRO

TRP

ALA

HIS

SER

LEU

GLY

SER

ARG

ASN

LEU

ALA

LEU

ALA

VAL

ALA

PRO

SER

SER

SER

SER

S43

�P44

�W45

�R46

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A50

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TYR

GLU

GLU

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ASP

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ARG

THR

GLU

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L227

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V231

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F243

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R274

F275

L276

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Chain k:

MET

ASN

GLY

ALA

LEU

GLY

LYS

ALA

LEU

CYS

LEU

ARG

ASN

ASP

THR

VAL

LEU

LYS

GLN

ALA

LEU

SER

LEU

ILE

ARG

VAL

ARG

ALA

SER

GLY

GLU

SER

PRO

ILE

CYS

SER

ALA

GLY

GLY

ILE

LEU

LEU

SER

THR

SER

ARG

HIS

Y48

Q66

�GLU

PRO

LYS

LYS

LYS

LYS

GLY

LYS

VAL

GLU

V77

�R78

�P79

�I80

�N81

�L82

�G83

�T84

�D85

�Y86

E87

�Y88

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L91

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GLU

GLN

GLY

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LYS

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L150�

T151�

T152

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G161

L162

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E188

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T190

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E192�

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LYS

GLY

ARG

PHE

LYS

ALA

ARG

PRO

GLU

LEU

GLU

GLU

LEU

LEU

ALA

LYS

LEU

ASN


Chain l:

MET

ALA

ALA

THR

VAL

LEU

CYS

GLY

VAL

LEU

ARG

ALA

TRP

ARG

THR

GLY

VAL

PRO

LEU

GLY

CYS

GLY

LEU

ARG

ARG

LEU

SER

GLN

THR

GLN

GLY

THR

PRO

E34

�Y35

�

R59

�

E64

�

D77

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S89

R90

N93

D99

I100

T101

N141

F166


Chain m:

MET

ALA

ALA

ARG

TRP

VAL

SER

GLY

LEU

ALA

ARG

ARG

SER

LEU

THR

CYS

ALA

VAL

SER

GLY

ALA

PRO

ARG

ARG

GLU

PHE

TRP

SER

PRO

PHE

ARG

LYS

GLU

LYS

GLN

PRO

VAL

VAL

ALA

GLU

THR

VAL

GLU

GLU

VAL

LYS

LYS

GLU

PRO

ILE

L51

�V52

�

P55

�I56

Q57

�S58

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E65

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�V83

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S85

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L97

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M121

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D142�

N148�

Y159


Chain n:

MET

ALA

GLY

SER

LEU

SER

TRP

VAL

THR

GLY

ARG

GLY

LEU

TRP

GLY

GLN

LEU

PRO

LEU

THR

CYS

ARG

SER

PHE

SER

LEU

GLY

ILE

PRO

ARG

LEU

F32

K42

�

R46

V56

N65

F66

I92

V98

R101

D105

R128


Chain o:

MET

ALA

ALA

TRP

GLY

ILE

LEU

LEU

SER

THR

GLY

VAL

ARG

ARG

LEU

HIS

CYS

GLY

THR

ALA

ALA

GLN

A23

Y40

L43

T44

D48

D53

�

R65

R76

E97

�K98

L99

�Q100�

E103�

K107�

K113�

L116�

LEU

GLN

ASN

PRO

GLN

PRO

SER

GLN


Chain p:

MET

A2

�A3

�A4

�L5

�A6

�R7

�L8

�G9

�L10

�R11

�

K14

�

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�

A36

�V37

�S38

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K41

�V42

R43

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�L47

�N48

�C49

�S50

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D54

�V55

R56

�H57

D58

�G59

S60

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F68

�G69

D70

�G71

�H72

�R73

�L74

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H80

�

E85

�M86

L87

�

A91

�S92

�

H93

I94�

Q95�

A96�

R97�

G98�

ALA

ALA

GLY

SER

GLY

ASP

LYS

PRO

SER

ALA

SER

THR

GLY

ARG



Chain q:

MET

ALA

ALA

ARG

ARG

LEU

PHE

GLY

ALA

ALA

ARG

SER

TRP

ALA

ALA

TRP

ARG

ALA

TRP

GLU

LEU

SER

ASP

ALA

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• Molecule 18: MITORIBOSOMAL PROTEIN ML63, MRPL57, MRP63

Chain t:

MET

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R9

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• Molecule 19: MITORIBOSOMAL PROTEIN ML62, MRPL58, ICT1

Chain u:

MET

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CYS

LEU

ARG

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GLY

LEU

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• Molecule 20: MITORIBOSOMAL PROTEIN ML64, MRPL59, CRIF1

Chain v:

MET

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PRO

VAL

GLN

GLN

ALA

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THR

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• Molecule 21: MITORIBOSOMAL PROTEIN ML65, MRPS30

Chain w:


MET

ALA

ALA

ALA

ARG

CYS

ARG

ARG

PHE

PRO

LEU

ARG

GLY

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GLY

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LEU

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• Molecule 22: MITORIBOSOMAL PROTEIN ML66, MRPS18A

Chain x:

MET

VAL

GLY

LEU

ASN

VAL

LEU

VAL

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GLY

CYS

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• Molecule 23: UNASSIGNED SECONDARY STRUCTURE ELEMENTS

Chain z:

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4 Experimental information iO

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C1 DepositorNumber of particles used 141675 DepositorResolution determination method Not providedCTF correction method PER DETECTOR FRAME DepositorMicroscope FEI TITAN KRIOS DepositorVoltage (kV) 300 DepositorElectron dose (e−/Å

2) 20 Depositor

Minimum defocus (nm) 800 DepositorMaximum defocus (nm) 3000 DepositorMagni�cation 100000 DepositorImage detector FEI FALCON II (4k x 4k) DepositorMaximum map value 0.560 DepositorMinimum map value -0.257 DepositorAverage map value 0.004 DepositorMap value standard deviation 0.025 DepositorRecommended contour level 0.07 DepositorMap size (Å) 302.4, 302.4, 302.4 wwPDBMap dimensions 216, 216, 216 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.4, 1.4, 1.4 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:ZN

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 0.34 0/3267 0.53 0/44552 b 0.36 0/3047 0.55 0/41393 c 0.33 0/2464 0.50 0/33304 d 0.38 0/853 0.56 1/1153 (0.1%)5 e 0.37 0/996 0.56 0/13406 f 0.38 0/731 0.54 0/9907 g 0.38 0/1191 0.58 0/16148 h 0.35 0/2372 0.53 0/32119 i 0.32 0/2034 0.52 0/275910 j 0.34 0/1811 0.56 0/243611 k 0.35 0/1070 0.55 0/144812 l 0.38 0/1135 0.53 0/154913 m 0.30 0/917 0.49 0/124814 n 0.44 0/860 0.60 0/115015 o 0.39 0/762 0.52 0/102216 p 0.34 0/752 0.53 0/101317 q 0.29 0/346 0.47 0/46318 t 0.41 0/798 0.61 0/107319 u 0.31 0/1163 0.49 0/155720 v 0.33 0/1022 0.44 0/138221 w 0.39 0/3206 0.55 0/435422 x 0.36 0/1364 0.62 0/1849All All 0.36 0/32161 0.54 1/43535 (0.0%)

Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifying ifthe center is modelled as a planar moiety or with the opposite hand.A planarity outlier is detectedby checking planarity of atoms in a peptide group, atoms in a mainchain group or atoms of asidechain that are expected to be planar.

Mol Chain #Chirality outliers #Planarity outliers2 b 0 1

Continued on next page...

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



Mol Chain #Chirality outliers #Planarity outliers10 j 0 114 n 0 121 w 0 1All All 0 4

There are no bond length outliers.

All (1) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)4 d 180 PRO C-N-CD -5.25 109.05 120.60

There are no chirality outliers.

All (4) planarity outliers are listed below:

Mol Chain Res Type Group2 b 210 GLU Peptide10 j 173 LEU Peptide14 n 65 ASN Peptide21 w 357 ASP Peptide

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 3173 0 3153 0 02 b 2952 0 2840 0 03 c 2408 0 2415 0 04 d 832 0 828 0 05 e 968 0 968 0 06 f 852 0 834 0 07 g 1167 0 1173 0 08 h 2319 0 2332 0 09 i 1979 0 1974 0 010 j 1775 0 1797 0 011 k 1050 0 1044 0 012 l 1097 0 1080 0 0


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



Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes13 m 893 0 878 0 014 n 837 0 860 0 015 o 747 0 748 0 016 p 742 0 749 0 017 q 336 0 342 0 018 t 780 0 792 0 019 u 1208 0 1227 0 020 v 1068 0 1034 0 021 w 3126 0 3153 0 022 x 1325 0 1354 0 023 z 282 0 294 0 024 x 1 0 0 0 0All All 31917 0 31869 0 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 12.

There are no clashes within the asymmetric unit.

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 391/423 (92%) 375 (96%) 16 (4%) 0 100 100

2 b 352/380 (93%) 329 (94%) 23 (6%) 0 100 100

3 c 293/334 (88%) 279 (95%) 14 (5%) 0 100 100

4 d 97/206 (47%) 92 (95%) 5 (5%) 0 100 100

5 e 119/135 (88%) 115 (97%) 4 (3%) 0 100 100

6 f 82/142 (58%) 81 (99%) 1 (1%) 0 100 100

7 g 146/159 (92%) 141 (97%) 5 (3%) 0 100 100Continued on next page...

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



Mol Chain Analysed Favoured Allowed Outliers Percentiles

8 h 287/332 (86%) 270 (94%) 17 (6%) 0 100 100

9 i 240/312 (77%) 230 (96%) 10 (4%) 0 100 100

10 j 211/279 (76%) 200 (95%) 9 (4%) 2 (1%) 17 49

11 k 125/212 (59%) 119 (95%) 6 (5%) 0 100 100

12 l 131/166 (79%) 127 (97%) 4 (3%) 0 100 100

13 m 107/159 (67%) 101 (94%) 6 (6%) 0 100 100

14 n 95/128 (74%) 91 (96%) 4 (4%) 0 100 100

15 o 92/124 (74%) 87 (95%) 5 (5%) 0 100 100

16 p 95/112 (85%) 90 (95%) 5 (5%) 0 100 100

17 q 35/138 (25%) 33 (94%) 2 (6%) 0 100 100

18 t 92/102 (90%) 88 (96%) 4 (4%) 0 100 100

19 u 137/205 (67%) 130 (95%) 7 (5%) 0 100 100

20 v 118/222 (53%) 116 (98%) 2 (2%) 0 100 100

21 w 385/433 (89%) 363 (94%) 20 (5%) 2 (0%) 29 61

22 x 160/196 (82%) 155 (97%) 4 (2%) 1 (1%) 25 57

All All 3790/4899 (77%) 3612 (95%) 173 (5%) 5 (0%) 54 82

All (5) Ramachandran outliers are listed below:

Mol Chain Res Type21 w 159 VAL22 x 93 ILE10 j 84 TYR10 j 151 ARG21 w 358 GLY

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.

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


Mol Chain Analysed Rotameric Outliers Percentiles

1 a 348/365 (95%) 332 (95%) 16 (5%) 27 57

2 b 310/328 (94%) 296 (96%) 14 (4%) 27 58

3 c 271/299 (91%) 260 (96%) 11 (4%) 30 59

4 d 92/181 (51%) 87 (95%) 5 (5%) 22 52

5 e 100/108 (93%) 94 (94%) 6 (6%) 19 49

6 f 80/110 (73%) 72 (90%) 8 (10%) 7 27

7 g 128/136 (94%) 113 (88%) 15 (12%) 5 20

8 h 251/284 (88%) 234 (93%) 17 (7%) 16 45

9 i 218/281 (78%) 211 (97%) 7 (3%) 39 67

10 j 190/242 (78%) 180 (95%) 10 (5%) 22 52

11 k 115/181 (64%) 111 (96%) 4 (4%) 36 65

12 l 122/147 (83%) 115 (94%) 7 (6%) 20 50

13 m 103/145 (71%) 101 (98%) 2 (2%) 57 78

14 n 88/113 (78%) 81 (92%) 7 (8%) 12 38

15 o 74/97 (76%) 68 (92%) 6 (8%) 11 38

16 p 79/88 (90%) 78 (99%) 1 (1%) 69 84

17 q 36/114 (32%) 36 (100%) 0 100 100

18 t 75/82 (92%) 67 (89%) 8 (11%) 6 24

19 u 126/169 (75%) 121 (96%) 5 (4%) 31 60

20 v 102/173 (59%) 99 (97%) 3 (3%) 42 69

21 w 340/373 (91%) 318 (94%) 22 (6%) 17 46

22 x 149/173 (86%) 139 (93%) 10 (7%) 16 46

All All 3397/4189 (81%) 3213 (95%) 184 (5%) 26 52

All (184) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 a 35 VAL1 a 113 LEU1 a 151 ASP1 a 175 THR1 a 195 HIS1 a 207 ASN1 a 210 SER1 a 225 SER




Mol Chain Res Type1 a 248 THR1 a 268 CYS1 a 270 VAL1 a 274 ASN1 a 277 THR1 a 335 VAL1 a 348 ASP1 a 398 VAL2 b 53 SER2 b 143 CYS2 b 157 LEU2 b 173 LEU2 b 209 ASP2 b 210 GLU2 b 237 VAL2 b 267 ARG2 b 281 PHE2 b 288 SER2 b 321 CYS2 b 324 ASP2 b 350 TYR2 b 360 ARG3 c 56 THR3 c 106 ASP3 c 131 ASP3 c 140 TRP3 c 149 CYS3 c 211 LEU3 c 222 VAL3 c 272 CYS3 c 280 VAL3 c 285 THR3 c 310 ASN4 d 99 ARG4 d 136 ILE4 d 139 LEU4 d 150 LEU4 d 168 LEU5 e 19 SER5 e 66 PHE5 e 78 GLU5 e 106 THR




Mol Chain Res Type5 e 111 HIS5 e 127 GLN6 f 44 ASN6 f 59 VAL6 f 64 SER6 f 72 THR6 f 103 LEU6 f 120 LYS6 f 122 ARG6 f 131 ARG7 g 6 THR7 g 9 ARG7 g 14 VAL7 g 21 ARG7 g 28 ARG7 g 33 LEU7 g 34 SER7 g 39 SER7 g 70 CYS7 g 94 VAL7 g 108 SER7 g 112 VAL7 g 114 ARG7 g 126 ILE7 g 138 THR8 h 33 LYS8 h 51 LEU8 h 78 ARG8 h 88 LEU8 h 98 ILE8 h 133 SER8 h 148 LEU8 h 167 CYS8 h 171 ARG8 h 181 SER8 h 191 LEU8 h 192 ARG8 h 211 THR8 h 216 ARG8 h 232 TRP8 h 288 THR8 h 301 LEU




Mol Chain Res Type9 i 81 THR9 i 100 LEU9 i 134 ILE9 i 151 CYS9 i 165 THR9 i 215 ARG9 i 258 SER10 j 55 ARG10 j 145 ASP10 j 231 VAL10 j 255 VAL10 j 262 ASP10 j 264 LEU10 j 265 LYS10 j 274 ARG10 j 276 LEU10 j 277 LEU11 k 77 VAL11 k 98 TYR11 k 151 THR11 k 162 LEU12 l 89 SER12 l 90 ARG12 l 93 ASN12 l 99 ASP12 l 100 ILE12 l 101 THR12 l 141 ASN13 m 90 ILE13 m 121 MET14 n 46 ARG14 n 56 VAL14 n 66 PHE14 n 92 ILE14 n 98 VAL14 n 101 ARG14 n 105 ASP15 o 40 TYR15 o 43 LEU15 o 44 THR15 o 48 ASP15 o 65 ARG




Mol Chain Res Type15 o 76 ARG16 p 60 SER18 t 9 ARG18 t 25 ARG18 t 45 ASN18 t 49 LEU18 t 51 ARG18 t 82 PHE18 t 86 ARG18 t 101 TRP19 u 79 SER19 u 97 LYS19 u 123 LYS19 u 137 GLU19 u 140 ARG20 v 53 SER20 v 64 HIS20 v 68 SER21 w 59 ARG21 w 81 ARG21 w 100 LEU21 w 104 ASN21 w 126 GLU21 w 162 ASP21 w 166 ILE21 w 205 LEU21 w 236 ARG21 w 245 VAL21 w 263 ASP21 w 267 LEU21 w 271 GLN21 w 274 ASN21 w 287 CYS21 w 335 MET21 w 395 LEU21 w 399 ILE21 w 404 VAL21 w 405 LYS21 w 420 LEU21 w 421 ASN22 x 54 THR22 x 56 THR




Mol Chain Res Type22 x 70 CYS22 x 72 ILE22 x 92 PHE22 x 111 GLU22 x 115 ILE22 x 118 CYS22 x 121 MET22 x 149 ARG

Sometimes sidechains can be �ipped to improve hydrogen bonding and reduce clashes. All (59)such sidechains are listed below:

Mol Chain Res Type1 a 96 HIS1 a 108 HIS1 a 156 ASN1 a 223 HIS1 a 274 ASN1 a 289 HIS1 a 343 GLN1 a 360 ASN1 a 420 HIS2 b 220 ASN2 b 224 HIS2 b 266 HIS2 b 308 GLN2 b 320 GLN3 c 281 HIS3 c 294 GLN3 c 305 HIS3 c 310 ASN6 f 44 ASN6 f 121 HIS6 f 130 HIS7 g 17 ASN7 g 120 HIS7 g 131 HIS8 h 94 ASN8 h 177 GLN8 h 260 GLN9 i 115 ASN9 i 157 HIS9 i 193 GLN




Mol Chain Res Type9 i 196 GLN9 i 217 HIS9 i 274 GLN11 k 61 HIS11 k 177 ASN12 l 93 ASN12 l 141 ASN13 m 107 ASN14 n 69 HIS14 n 122 ASN14 n 124 HIS15 o 63 GLN16 p 72 HIS16 p 93 HIS18 t 34 ASN18 t 45 ASN18 t 85 HIS19 u 103 HIS19 u 145 ASN21 w 101 ASN21 w 104 ASN21 w 173 GLN21 w 228 ASN21 w 233 ASN21 w 234 GLN21 w 367 GLN21 w 385 ASN22 x 164 ASN22 x 184 ASN

5.3.3 RNA iO

There are no RNA molecules in this entry.

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.

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


5.6 Ligand geometry iO

Of 1 ligands modelled in this entry, 1 is monoatomic - leaving 0 for Mogul analysis.

There are no bond length outliers.

There are no bond angle outliers.

There are no chirality outliers.

There are no torsion outliers.

There are no ring outliers.

No monomer is involved in short contacts.

5.7 Other polymers iO

There are no such residues in this entry.

5.8 Polymer linkage issues iO

The following chains have linkage breaks:

Mol Chain Number of breaks23 z 520 v 1

All chain breaks are listed below:

Model Chain Residue-1 Atom-1 Residue-2 Atom-2 Distance (Å)1 z 36:UNK C 99:UNK N 57.051 z 106:UNK C 201:UNK N 13.001 z 105:UNK C 106:UNK N 3.371 v 154:UNK C 155:UNK N 3.121 z 35:UNK C 36:UNK N 3.121 z 210:UNK C 211:UNK N 3.12

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


6 Map visualisation iO

This section contains visualisations of the EMDB entry EMD-2787. These allow visual inspectionof the internal detail of the map and identi�cation of artifacts.

No raw map or half-maps were deposited for this entry and therefore no images, graphs, etc.pertaining to the raw map can be shown.

6.1 Orthogonal projections iO

6.1.1 Primary map

X Y Z

The images above show the map projected in three orthogonal directions.

6.2 Central slices iO

6.2.1 Primary map

X Index: 108 Y Index: 108 Z Index: 108

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


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

6.3 Largest variance slices iO

6.3.1 Primary map

X Index: 120 Y Index: 86 Z Index: 98

The images above show the largest variance slices of the map in three orthogonal directions.

6.4 Orthogonal surface views iO

6.4.1 Primary map

X Y Z

The images above show the 3D surface view of the map at the recommended contour level 0.07.These images, in conjunction with the slice images, may facilitate assessment of whether an ap-propriate contour level has been provided.

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


6.5 Mask visualisation iO

This section was not generated. No masks/segmentation were deposited.

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


7.2 Volume estimate iO

The volume at the recommended contour level is 700 nm3; this corresponds to an approximatemass of 632 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

*Reported resolution corresponds to spatial frequency of 0.294 Å−1

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-2787 and PDBmodel 4V1A. Per-residue inclusion information can be found in section 3 on page 8.

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 0.07 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_fithttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_overlay


9.2 Atom inclusion iO

At the recommended contour level, 80% of all backbone atoms, 66% of all non-hydrogen atoms,are inside the map.

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

Overall quality at a glanceEntry compositionResidue-property plotsExperimental informationModel qualityStandard geometryToo-close contactsTorsion anglesProtein backboneProtein sidechainsRNA

Non-standard residues in protein, DNA, RNA chainsCarbohydratesLigand geometryOther polymersPolymer linkage issues

Map visualisationOrthogonal projectionsPrimary map

Central slicesPrimary map

Largest variance slicesPrimary map

Orthogonal surface viewsPrimary map

Mask visualisation

Map analysisMap-value distributionVolume estimateRotationally averaged power spectrum

Fourier-Shell correlationMap-model fitMap-model overlayAtom inclusion

Full wwPDB EM Validation Report O i...N.; Aebersold, R.; Ban, N. Deposited on : 2014-09-25...

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