full wwpdb em validation report i - rcsb · 2020. 12. 13. · page5 fullwwpdbemvalidationreport...

Full wwPDB EM Validation Report i○

Dec 12, 2020 – 10:32 PM EST

PDB ID : 6C6TEMDB ID : EMD-7350

Title : CryoEM structure of E.coli RNA polymerase elongation complex bound withRfaH

Authors : Kang, J.Y.; Artsimovitch, I.; Landick, R.; Darst, S.A.Deposited on : 2018-01-19

Resolution : 3.50 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 specific help available everywhere you see the i○ symbol.

The following versions of software and data (see references i○) 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/EMValidationReportHelp



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

Full wwPDB EM Validation Report EMD-7350, 6C6T

1 Overall quality at a glance i○

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

The reported resolution of this entry is 3.50 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.

Metric Whole archive(#Entries)

EM structures(#Entries)

Clashscore 158937 4297Ramachandran outliers 154571 4023

Sidechain outliers 154315 3826RNA backbone 4643 859

The table below summarises the geometric issues observed across the polymeric chains and their fitto 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 <=5%The upper red bar (where present) indicates the fraction of residues that have poor fit to the EMmap (all-atom inclusion < 40%). The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 A 29

2 B 29

3 R 20

4 G 239

4 H 239

5 I 1342

6 J 1407Continued on next page...

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


Continued from previous page...Mol Chain Length Quality of chain

7 K 91

8 D 162


2 Entry composition i○

There are 10 unique types of molecules in this entry. The entry contains 26915 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 DNA chain called DNA (29-MER).

Mol Chain Residues Atoms AltConf Trace

1 A 29 Total C N O P598 282 117 171 28 0 0

• Molecule 2 is a DNA chain called DNA (29-MER).


2 B 29 Total C N O P585 279 102 176 28 0 0

• Molecule 3 is a RNA chain called RNA (5’-R(*GP*CP*AP*UP*UP*CP*AP*AP*AP*GP*CP*CP*GP*AP*GP*AP*GP*GP*UP*A)-3’).


3 R 10 Total C N O P218 97 43 68 10 0 0

• Molecule 4 is a protein called DNA-directed RNA polymerase subunit alpha.


4 G 221 Total C N O S1694 1061 296 331 6 0 0

4 H 219 Total C N O S1687 1053 298 330 6 0 0

There are 10 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceG 235 GLU - expression tag UNP P0A7Z4G 236 VAL - expression tag UNP P0A7Z4G 237 LEU - expression tag UNP P0A7Z4G 238 PHE - expression tag UNP P0A7Z4G 239 GLN - expression tag UNP P0A7Z4H 235 GLU - expression tag UNP P0A7Z4

Continued on next page...

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


Continued from previous page...Chain Residue Modelled Actual Comment Reference

H 236 VAL - expression tag UNP P0A7Z4H 237 LEU - expression tag UNP P0A7Z4H 238 PHE - expression tag UNP P0A7Z4H 239 GLN - expression tag UNP P0A7Z4

• Molecule 5 is a protein called DNA-directed RNA polymerase subunit beta.


5 I 1319 Total C N O S10407 6530 1814 2020 43 0 0

• Molecule 6 is a protein called DNA-directed RNA polymerase subunit beta’.


6 J 1335 Total C N O S10388 6526 1854 1958 50 0 0

• Molecule 7 is a protein called DNA-directed RNA polymerase subunit omega.


7 K 83 Total C N O S655 399 123 132 1 0 0

• Molecule 8 is a protein called Transcription antitermination protein RfaH.


8 D 85 Total C N O S680 438 119 120 3 0 0

• Molecule 9 is MAGNESIUM ION (three-letter code: MG) (formula: Mg).

Mol Chain Residues Atoms AltConf

9 R 1 Total Mg1 1 0

• Molecule 10 is ZINC ION (three-letter code: ZN) (formula: Zn).

Mol Chain Residues Atoms AltConf

10 J 2 Total Zn2 2 0


3 Residue-property plots i○

These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. Thefirst 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 fit 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: DNA (29-MER)

Chain A:

G1�

G2 G3 G9 T10

A11

G12

C13

G14

T15

G16

G20

C21

C29

• Molecule 2: DNA (29-MER)

Chain B:

G1 A5 T15

A16

T21

C24

C29

• Molecule 3: RNA (5’-R(*GP*CP*AP*UP*UP*CP*AP*AP*AP*GP*CP*CP*GP*AP*GP*AP*GP*GP*UP*A)-3’)

Chain R:

G C A U U C A A A G C11

A14

G15

A16

A20

• Molecule 4: DNA-directed RNA polymerase subunit alpha

Chain G:

MET

GLN

GLY

SER

VAL

THR

E7 I16

V26

T27

L28

L43

R44

R45

P52

I61

V64

I78

L82

L100

K104

V110

T111

I115

G119

V129

I159

HIS

SER

GLU

GLU

ASP

GLU

ARG

P167

L171

R182

I183

A190

R195

L198

D199

K200

L201

I217

R218

R219

L228

F231

L234

GLU

VAL

LEU

PHE

GLN

• Molecule 4: DNA-directed RNA polymerase subunit alpha

Chain H:

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


MET

GLN

GLY

S4 R12

D15

V19

S20

T27

L28

R33

G34

F35

G36

H37

T38

R45

L48

S49

T57

I61

D62

G63

V64

E67

L79

L83

K86

A89

V90

R91

V92

Q93

G94

I99

L100

T101

L102

N103

K104

V110

T111

D114

V121

E122

V129

S141

M142

R143

G151

A155

R158

ILE

HIS

SER

GLU

GLU

ASP

GLU

ARG

PRO

ILE

G169

R170

L171

D174

A175

C176

Y177

S178

R182

I183

A184

Y185

E188

R191

V192

E193

D197

K200

L201

V202

M205

E206

T210

I211

D212

L224

F231

V232

ASP

LEU

GLU

VAL

LEU

PHE

GLN

• Molecule 5: DNA-directed RNA polymerase subunit beta

Chain I:

MET

V2 T6 K9 R10

D14

P19

V24

L27

I39

Q46

Y47

S55

V56

L68

Q69

L75

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P110

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PRO

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ASP

V913

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A128

0

T128

6L1

287

M129

0

H131

3Q1

314

P131

7

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2

• Molecule 6: DNA-directed RNA polymerase subunit beta’


Chain J:ME

TLY

SAS

PLE

ULE

ULY

SPH

ELE

ULY

SAL

AGL

NTH

RLY

STH

RGL

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6

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R53

C58

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C70

L71

C72

G73

K76

R77

L78

K79

G82

C85

E86

V92

V97

R98

R99

E100

R101

I114

L120

P121

S122

R123

L126

L127

L132

R137

V138

L139

Y140

F141

E142

S143

Y144

R156

D174

�

G181

S191

L201

N209

R214

T218

K219

R220

I221

K222

L223

L224

S230

G231

P246

L249

R275

R278

L279

I291

V292

R293

L299

D304

R312

G313

S319

N320

L342

L343

G351

R352

L363

H364

K370

R388

T393

I394

K395

A396

L412

D413

E414

V415

I416

R417

P420

V421

R425

A426

A436

F437

L441

V453

N458

F461

A467

M485

L491

S503

V506

V507

L508

G509

L510

M513

T514

R515

D516

V526

K531

E532

A533

E534

L544

K549

V550

D558

�A5

59

E562

S568

L569

K570

R576

L579

G586

N593

L596

I601

L605

Y609

R610

I611

L612

P616

I619

G628

A633

S638

V639

P647

Q665

R678

I683

M697

R709

V717

S718

S721

M724

R731

A741

L746

K749

P750

I754

I755

P758

I759

N762

L770

Q771

I774

H777

D785

K789

Y795

L796

T797

R798

R799

L800

V801

D802

V803

A804

Q805

D806

V809

C814

I820

P824

E827

�

D830

�V8

31K8

32E8

33P8

34L8

35R8

36

V839

R842

D847

V848

L849

K850

D855

I856

L857

V858

L864

R883

S884

D891

V894

D902

L903

A904

R905

G906

H907

I908

I909

I918

A919

A920

G924

E925

P926

L930

R933

THR

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HIS

ILE

GLY

GLY

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ALA

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S948

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3

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7

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1

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8

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2D1

273

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290

E129

3

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305

L130

6

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1

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325

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6

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0

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9

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9M1

370

R137

1R1

372

R137

3AL

AAL

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APR

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A

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PRO

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VAL

THR

ALA

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ASP

ALA

SER

ALA

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LEU

ALA

GLU

LEU

LEU

ASN

ALA

GLY

LEU

GLY

GLY

SER

ASP

ASN

GLU

• Molecule 7: DNA-directed RNA polymerase subunit omega

Chain K:


MET

A2 R3 V4 T5 R25

R26

A27

R28

Q29

M30

Q31

V32

K35

N43

A50

I54

E55

D65

V66

R67

A78

�E7

9�

L80

Q81

�

T84

�AL

AIL

EAL

AGL

UGL

YAR

GAR

G

• Molecule 8: Transcription antitermination protein RfaH

Chain D:

MET

Q2 S3 W4 R16

N27

C28

L29

T34

LEU

GLU

LYS

ILE

VAL

ARG

GLY

LYS

ARG

THR

ALA

VAL

S47

P52

N53

Y54

L55

F56

V57

E58

F59

H65

T66

T67

T68

I69

N70

R73

I93

V98

TYR

LYS

PRO

LYS

ASP

ILE

VAL

ASP

PRO

ALA

THR

PRO

TYR

PRO

GLY

ASP

LYS

VAL

ILE

ILE

THR

GLU

GLY

ALA

PHE

GLU

GLY

PHE

GLN

ALA

ILE

PHE

THR

GLU

PRO

ASP

GLY

GLU

ALA

ARG

SER

MET

LEU

LEU

LEU

ASN

LEU

ILE

ASN

LYS

GLU

ILE

LYS

HIS

SER

VAL

LYS

ASN

THR

GLU

PHE

ARG

LYS

LEU


4 Experimental information i○

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C1 DepositorNumber of particles used 174600 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−/Å2

) 71.0 DepositorMinimum defocus (nm) 500 DepositorMaximum defocus (nm) 3000 DepositorMagnification 38462 DepositorImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 0.185 DepositorMinimum map value -0.106 DepositorAverage map value 0.000 DepositorMap value standard deviation 0.005 DepositorRecommended contour level 0.016 DepositorMap size (Å) 332.8, 332.8, 332.8 wwPDBMap dimensions 256, 256, 256 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.3, 1.3, 1.3 Depositor

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


5 Model quality i○

5.1 Standard geometry i○

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

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 Chain Bond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >5

1 A 0.92 0/672 1.00 2/1037 (0.2%)2 B 1.03 0/653 1.03 0/10053 R 0.90 0/244 0.98 0/3794 G 0.48 0/1714 0.67 1/2323 (0.0%)4 H 0.41 0/1706 0.68 0/23115 I 0.50 0/10573 0.64 2/14265 (0.0%)6 J 0.48 0/10545 0.65 2/14236 (0.0%)7 K 0.41 0/657 0.66 0/8868 D 0.49 0/698 0.61 0/951All All 0.52 0/27462 0.68 7/37393 (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 outliers5 I 0 96 J 0 57 K 0 1All All 0 15

There are no bond length outliers.

All (7) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)6 J 903 LEU C-N-CA 5.86 136.36 121.704 G 61 ILE CG1-CB-CG2 -5.65 98.96 111.406 J 363 LEU CA-CB-CG 5.59 128.16 115.305 I 1233 LEU CA-CB-CG 5.46 127.85 115.30


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

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


Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 A 2 DG O4’-C4’-C3’ -5.38 102.35 104.501 A 11 DA P-O3’-C3’ 5.11 125.84 119.705 I 817 LEU CB-CG-CD2 -5.11 102.32 111.00

There are no chirality outliers.

All (15) planarity outliers are listed below:

Mol Chain Res Type Group5 I 1134 GLN Peptide5 I 1157 GLN Peptide5 I 1158 LYS Peptide5 I 205 PRO Peptide5 I 594 VAL Peptide5 I 595 THR Peptide5 I 596 ASP Mainchain5 I 696 ASP Peptide5 I 746 ALA Peptide6 J 1184 ASP Peptide6 J 1326 GLN Peptide6 J 313 GLY Peptide6 J 416 ILE Peptide6 J 804 ALA Peptide7 K 32 VAL Peptide

5.2 Too-close contacts i○

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 598 0 325 8 02 B 585 0 328 5 03 R 218 0 109 3 04 G 1694 0 1722 21 04 H 1687 0 1722 40 05 I 10407 0 10420 157 06 J 10388 0 10611 182 07 K 655 0 663 15 08 D 680 0 671 10 0


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


Continued from previous page...Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes9 R 1 0 0 0 010 J 2 0 0 0 0All All 26915 0 26571 396 0

The all-atom clashscore is defined as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 7.

All (396) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

6:J:425:ARG:NH1 6:J:458:ASN:O 2.08 0.867:K:3:ARG:NH1 7:K:55:GLU:OE2 2.09 0.84

6:J:665:GLN:HE22 6:J:678:ARG:HH11 1.25 0.845:I:1314:GLN:HB2 7:K:28:ARG:HH12 1.43 0.836:J:40:LYS:NZ 6:J:42:GLU:OE1 2.15 0.805:I:118:LYS:NZ 5:I:487:LEU:O 2.14 0.805:I:915:ASP:OD2 5:I:919:ARG:NH2 2.15 0.805:I:611:GLU:OE2 5:I:637:ARG:NH2 2.13 0.796:J:1169:THR:OG1 6:J:1192:LYS:NZ 2.13 0.796:J:201:LEU:HD11 6:J:220:ARG:HH11 1.46 0.784:H:182:ARG:NH1 6:J:534:GLU:OE1 2.16 0.786:J:1075:ARG:NH2 6:J:1168:GLU:OE2 2.17 0.775:I:1246:ARG:HH11 5:I:1266:GLY:HA2 1.50 0.775:I:1272:GLU:OE2 6:J:798:ARG:NH1 2.19 0.756:J:1143:ASP:OD1 6:J:1148:ARG:NH1 2.21 0.725:I:941:LYS:NZ 5:I:949:GLU:OE1 2.20 0.72

5:I:207:THR:OG1 5:I:354:ASP:OD2 2.09 0.715:I:19:PRO:HA 5:I:1156:ARG:HD3 1.73 0.706:J:77:ARG:HG3 6:J:79:LYS:H 1.58 0.682:B:16:DA:H1’ 6:J:426:ALA:HB1 1.74 0.674:H:86:LYS:NZ 6:J:532:GLU:OE2 2.22 0.675:I:339:ASN:HB3 5:I:343:HIS:H 1.59 0.678:D:27:ASN:HB2 8:D:58:GLU:HB3 1.77 0.675:I:802:VAL:HA 5:I:1096:ILE:O 1.93 0.66

6:J:1355:ARG:NH1 6:J:1369:ARG:HH12 1.93 0.666:J:1037:PHE:HB3 6:J:1040:MET:HB2 1.78 0.666:J:984:LEU:HB3 6:J:993:GLU:HB2 1.77 0.655:I:9:LYS:HG2 5:I:1171:ARG:NH1 2.11 0.655:I:118:LYS:NZ 5:I:485:ASP:OD1 2.25 0.655:I:878:THR:N 5:I:881:ASP:OD2 2.24 0.65

4:H:33:ARG:HH11 5:I:1081:PRO:HG3 1.60 0.65Continued on next page...


Continued from previous page...


Clashoverlap (Å)

5:I:9:LYS:HG2 5:I:1171:ARG:HH12 1.61 0.656:J:975:ILE:HG22 6:J:977:SER:H 1.62 0.656:J:978:ARG:HG2 6:J:1197:ASN:HD21 1.60 0.656:J:832:LYS:C 6:J:1242:ARG:HH12 2.01 0.64

4:H:33:ARG:NH1 5:I:1081:PRO:HG3 2.13 0.645:I:529:ARG:HH11 5:I:572:ILE:HG22 1.62 0.638:D:2:GLN:HA 8:D:59:PHE:O 1.98 0.637:K:29:GLN:HB3 7:K:35:LYS:HD2 1.80 0.636:J:58:CYS:SG 6:J:59:ALA:N 2.72 0.63

6:J:122:SER:HB2 6:J:132:LEU:HD12 1.81 0.636:J:1108:GLN:NE2 6:J:1123:ARG:HH11 1.97 0.636:J:1355:ARG:NH1 6:J:1369:ARG:NH1 2.47 0.626:J:156:ARG:NH2 6:J:191:SER:OG 2.33 0.626:J:201:LEU:HD11 6:J:220:ARG:NH1 2.15 0.624:G:28:LEU:HD22 4:G:201:LEU:HD23 1.80 0.615:I:1223:ARG:NH2 6:J:721:SER:OG 2.33 0.616:J:416:ILE:HG13 6:J:441:LEU:HD11 1.83 0.615:I:660:VAL:HG13 5:I:661:VAL:HG13 1.83 0.616:J:342:LEU:HD23 6:J:1352:ILE:HG23 1.83 0.606:J:370:LYS:HG2 6:J:441:LEU:HD23 1.84 0.601:A:13:DC:OP2 1:A:14:DG:N2 2.35 0.605:I:528:ARG:NH2 5:I:576:SER:O 2.34 0.606:J:951:GLN:NE2 6:J:1014:GLY:O 2.34 0.606:J:1161:GLY:HA3 6:J:1179:PRO:HA 1.83 0.606:J:412:LEU:HD22 6:J:441:LEU:HD21 1.84 0.605:I:953:LEU:HD11 5:I:1033:ARG:HG2 1.83 0.604:G:82:LEU:HD11 4:G:171:LEU:HD23 1.84 0.596:J:73:GLY:O 6:J:76:LYS:NZ 2.35 0.59

6:J:1350:ASN:HD22 6:J:1358:PRO:HD3 1.67 0.597:K:26:ARG:NH1 7:K:67:ARG:HH12 2.00 0.595:I:1142:ARG:NH2 5:I:1166:ASP:OD1 2.36 0.59

3:R:16:A:OP2 5:I:540:ARG:NH2 2.36 0.596:J:514:THR:HG21 6:J:596:LEU:HD12 1.84 0.595:I:478:ARG:NH1 5:I:491:ASP:O 2.34 0.594:G:43:LEU:HD13 4:G:217:ILE:HD11 1.84 0.586:J:275:ARG:NH1 6:J:278:ARG:NH1 2.51 0.586:J:665:GLN:HE22 6:J:678:ARG:NH1 1.99 0.585:I:839:VAL:HG12 5:I:1049:ILE:HG12 1.83 0.585:I:1184:THR:HG23 5:I:1190:ALA:H 1.67 0.586:J:638:SER:OG 6:J:639:VAL:N 2.36 0.586:J:491:LEU:HB2 6:J:904:ALA:HA 1.86 0.58





Clashoverlap (Å)

6:J:85:CYS:SG 6:J:86:GLU:N 2.76 0.585:I:400:VAL:HG11 5:I:452:ARG:HD2 1.86 0.586:J:926:PRO:HG2 6:J:1248:ILE:HD11 1.84 0.586:J:510:LEU:HD22 6:J:601:ILE:HD12 1.86 0.576:J:795:TYR:OH 6:J:1326:GLN:NE2 2.36 0.575:I:10:ARG:NH1 5:I:697:LYS:HD3 2.19 0.575:I:840:SER:HB2 5:I:850:ILE:HD11 1.87 0.576:J:774:ILE:HA 6:J:777:HIS:HD2 1.70 0.57

5:I:818:VAL:HG22 5:I:1096:ILE:HG12 1.86 0.576:J:741:ALA:O 6:J:762:ASN:ND2 2.38 0.57

6:J:343:LEU:HD11 6:J:1324:SER:HB3 1.87 0.575:I:1072:ASN:ND2 5:I:1111:GLN:OE1 2.37 0.565:I:1246:ARG:NH1 5:I:1266:GLY:HA2 2.19 0.566:J:903:LEU:HD21 6:J:1249:ASN:HD22 1.70 0.566:J:388:ARG:NH2 6:J:414:GLU:OE1 2.38 0.566:J:218:THR:HA 6:J:221:ILE:HG22 1.87 0.565:I:227:LYS:NZ 5:I:298:ALA:HB1 2.21 0.56

6:J:1046:ILE:HD12 6:J:1059:LEU:HB3 1.86 0.565:I:174:ALA:HB2 5:I:432:LEU:HD13 1.88 0.565:I:241:LEU:HD21 5:I:246:LEU:HD11 1.88 0.556:J:120:LEU:O 6:J:1330:ARG:NH1 2.39 0.556:J:70:CYS:SG 6:J:71:LEU:N 2.79 0.55

5:I:801:ARG:HG2 5:I:1094:VAL:HG23 1.87 0.554:H:191:ARG:NH2 4:H:193:GLU:O 2.39 0.555:I:39:ILE:HD12 5:I:75:LEU:HD22 1.88 0.556:J:139:LEU:HA 6:J:181:GLY:HA2 1.88 0.555:I:449:GLY:HA3 5:I:609:ILE:HG23 1.88 0.555:I:218:GLU:OE2 5:I:300:ASP:N 2.28 0.556:J:144:TYR:OH 6:J:293:ARG:NH2 2.40 0.556:J:833:GLU:HB2 6:J:1242:ARG:NH1 2.22 0.554:H:100:LEU:HD21 4:H:121:VAL:HG11 1.88 0.555:I:1246:ARG:NH1 5:I:1258:PRO:HB3 2.22 0.556:J:1175:LEU:HD22 6:J:1190:ILE:HD11 1.88 0.554:H:28:LEU:HD12 4:H:201:LEU:HD23 1.88 0.546:J:1155:ILE:HG13 6:J:1210:ILE:HB 1.88 0.541:A:10:DT:H2” 8:D:68:THR:HG23 1.89 0.54

6:J:1166:GLY:HA3 6:J:1174:ARG:HB2 1.88 0.545:I:1275:VAL:HG13 5:I:1287:LEU:HD11 1.90 0.545:I:699:LEU:HG 5:I:799:ASN:HD22 1.71 0.546:J:814:CYS:SG 6:J:883:ARG:NH2 2.81 0.546:J:123:ARG:O 6:J:127:LEU:HB2 2.07 0.54





Clashoverlap (Å)

5:I:1254:VAL:O 6:J:99:ARG:NH2 2.40 0.544:H:206:GLU:OE1 6:J:531:LYS:NZ 2.38 0.536:J:802:ASP:OD1 6:J:1348:LYS:NZ 2.31 0.536:J:804:ALA:O 6:J:806:ASP:N 2.41 0.53

5:I:1287:LEU:HD13 6:J:1357:ILE:HD11 1.90 0.535:I:1069:ARG:NH2 5:I:1114:GLU:OE2 2.30 0.536:J:759:ILE:HG23 6:J:771:GLN:HB3 1.90 0.536:J:785:ASP:O 6:J:789:LYS:HB2 2.08 0.53

4:G:104:LYS:HG2 4:G:110:VAL:HG22 1.91 0.534:G:111:THR:HA 4:G:129:VAL:HA 1.91 0.535:I:866:ASP:OD2 5:I:944:ARG:HD2 2.09 0.531:A:3:DG:OP2 6:J:46:TYR:OH 2.27 0.53

5:I:1246:ARG:NH2 5:I:1250:SER:O 2.35 0.536:J:746:LEU:HG 6:J:758:PRO:HG3 1.90 0.535:I:808:ASN:H 6:J:633:ALA:HB2 1.74 0.525:I:628:HIS:HB3 5:I:647:ARG:HH21 1.74 0.524:H:104:LYS:NZ 4:H:114:ASP:OD2 2.23 0.522:B:5:DA:OP2 6:J:1172:LYS:NZ 2.34 0.52

7:K:26:ARG:HH12 7:K:67:ARG:HH12 1.56 0.526:J:832:LYS:HB3 6:J:1242:ARG:NH1 2.24 0.526:J:850:LYS:HB2 6:J:857:LEU:HB2 1.91 0.524:G:28:LEU:HB2 4:G:201:LEU:HB3 1.92 0.525:I:657:THR:HG21 5:I:1188:ASP:HB2 1.92 0.525:I:813:GLU:HB2 6:J:461:PHE:HD2 1.74 0.525:I:835:GLU:OE2 5:I:1051:LYS:HD3 2.08 0.526:J:975:ILE:HD11 6:J:1003:LEU:HD11 1.91 0.526:J:805:GLN:HE21 6:J:1348:LYS:HB2 1.75 0.515:I:242:VAL:HB 5:I:245:ARG:NH1 2.24 0.51

5:I:817:LEU:HD12 5:I:1078:LYS:HB3 1.93 0.514:G:16:ILE:HG12 4:G:26:VAL:HG12 1.92 0.514:H:48:LEU:HB2 4:H:183:ILE:HD11 1.93 0.518:D:27:ASN:O 8:D:57:VAL:HA 2.10 0.51

5:I:689:ALA:HB2 5:I:1233:LEU:HD23 1.93 0.516:J:437:PHE:HZ 6:J:453:VAL:HG11 1.76 0.516:J:683:ILE:HD12 6:J:754:ILE:HG21 1.93 0.514:G:218:ARG:NH1 4:H:231:PHE:O 2.44 0.516:J:972:LYS:HD2 6:J:1004:ALA:HA 1.94 0.504:H:183:ILE:HG22 4:H:205:MET:HG3 1.92 0.506:J:1371:ARG:HE 6:J:1372:ARG:NH1 2.10 0.506:J:749:LYS:HB3 6:J:755:ILE:HD11 1.94 0.506:J:421:VAL:O 6:J:436:ALA:HA 2.12 0.50





Clashoverlap (Å)

7:K:26:ARG:NH1 7:K:67:ARG:NH1 2.59 0.503:R:20:A:O2’ 6:J:425:ARG:NH2 2.42 0.50

5:I:524:ILE:HG21 5:I:708:VAL:HG13 1.91 0.504:H:151:GLY:H 4:H:177:TYR:HB2 1.76 0.50

5:I:733:VAL:HG22 5:I:750:ILE:HG12 1.94 0.506:J:275:ARG:HH12 6:J:278:ARG:NH1 2.09 0.505:I:232:ILE:HD12 5:I:331:LYS:HA 1.94 0.506:J:82:GLY:H 6:J:92:VAL:HG13 1.77 0.50

5:I:998:LEU:HG 5:I:1011:LEU:HB3 1.94 0.504:H:57:THR:HA 4:H:175:ALA:HB2 1.94 0.495:I:1070:HIS:NE2 5:I:1114:GLU:OE1 2.36 0.494:G:100:LEU:HD23 4:G:115:ILE:HG21 1.93 0.495:I:103:VAL:HG12 5:I:117:ILE:HG22 1.94 0.494:H:83:LEU:HD11 6:J:526:VAL:HB 1.94 0.495:I:125:GLY:HA2 5:I:499:SER:HB2 1.94 0.496:J:799:ARG:HG2 6:J:1325:PHE:HZ 1.78 0.494:H:61:ILE:HB 4:H:64:VAL:HB 1.95 0.49

5:I:452:ARG:HH12 5:I:458:GLU:CD 2.15 0.496:J:800:LEU:HB3 6:J:920:ALA:HB1 1.95 0.496:J:393:THR:HG23 6:J:396:ALA:H 1.78 0.495:I:14:ASP:HA 5:I:1183:ALA:HB3 1.94 0.49

5:I:1314:GLN:HA 7:K:28:ARG:HH22 1.78 0.494:H:45:ARG:O 4:H:49:SER:HB2 2.12 0.48

5:I:24:VAL:HG22 5:I:578:TYR:HE1 1.78 0.484:H:67:GLU:HG3 4:H:171:LEU:HD22 1.95 0.485:I:1101:LEU:HD21 6:J:508:LEU:HD22 1.95 0.485:I:1102:GLY:HA2 5:I:1106:ARG:NH1 2.28 0.485:I:632:ASP:HA 5:I:647:ARG:HB2 1.94 0.486:J:550:VAL:O 6:J:569:LEU:HA 2.13 0.48

6:J:1027:VAL:HB 6:J:1121:LEU:HB2 1.96 0.485:I:726:TYR:HB3 5:I:733:VAL:HB 1.94 0.486:J:1347:LEU:HG 6:J:1357:ILE:HG23 1.96 0.484:G:228:LEU:HD21 4:H:224:LEU:HB3 1.96 0.485:I:529:ARG:HH22 5:I:687:ARG:NH1 2.11 0.486:J:1261:LEU:HD12 6:J:1304:ARG:HH21 1.79 0.486:J:809:VAL:HG21 6:J:909:ILE:HG12 1.95 0.487:K:4:VAL:HG22 7:K:5:THR:HG23 1.96 0.484:G:45:ARG:NH2 5:I:1215:GLY:O 2.41 0.476:J:833:GLU:N 6:J:1242:ARG:HH12 2.12 0.472:B:15:DT:H2’ 2:B:16:DA:C8 2.48 0.47

6:J:1060:VAL:HG13 6:J:1106:ILE:HG12 1.96 0.47Continued on next page...




Clashoverlap (Å)

6:J:891:ASP:OD2 6:J:1290:ARG:NH2 2.47 0.476:J:417:ARG:HH12 7:K:43:ASN:HB2 1.80 0.475:I:227:LYS:HZ2 5:I:298:ALA:HB1 1.78 0.475:I:559:CYS:HB2 5:I:662:SER:HB3 1.96 0.475:I:618:GLN:OE1 5:I:635:THR:OG1 2.32 0.475:I:746:ALA:HA 5:I:974:ARG:HH21 1.78 0.476:J:1167:LYS:NZ 6:J:1170:LYS:HB2 2.30 0.474:G:45:ARG:HG2 4:H:38:THR:HB 1.97 0.476:J:1036:ARG:HE 6:J:1081:VAL:HG11 1.79 0.476:J:1146:GLU:OE2 6:J:1310:THR:HG22 2.14 0.475:I:838:CYS:HB2 5:I:918:LEU:HD22 1.96 0.476:J:513:MET:HE1 6:J:579:LEU:HD13 1.96 0.475:I:618:GLN:HG3 6:J:770:LEU:HD13 1.95 0.477:K:26:ARG:HH12 7:K:67:ARG:NH1 2.13 0.476:J:209:ASN:OD1 6:J:214:ARG:NH2 2.48 0.476:J:526:VAL:HG12 6:J:549:LYS:HB2 1.97 0.475:I:1280:ALA:HB1 6:J:918:ILE:HG22 1.96 0.474:H:111:THR:HG22 4:H:129:VAL:HA 1.96 0.46

5:I:318:SER:H 5:I:321:LEU:HD12 1.80 0.466:J:968:ASN:HA 6:J:1117:SER:HB2 1.96 0.46

6:J:1221:LEU:HD22 6:J:1306:LEU:HB2 1.96 0.466:J:319:SER:HA 6:J:320:ASN:HA 1.64 0.465:I:27:LEU:O 5:I:528:ARG:NH1 2.43 0.46

5:I:641:GLU:OE2 6:J:749:LYS:NZ 2.47 0.465:I:549:ASP:OD2 6:J:750:PRO:HB3 2.15 0.468:D:29:LEU:HB3 8:D:56:PHE:HB2 1.97 0.464:H:93:GLN:HG3 4:H:94:GLY:H 1.81 0.466:J:1150:PRO:HG3 6:J:1214:PRO:HB2 1.97 0.466:J:902:ASP:OD2 6:J:905:ARG:HB2 2.15 0.464:H:104:LYS:HD3 4:H:110:VAL:HG22 1.96 0.465:I:685:MET:SD 5:I:1073:LYS:HG2 2.55 0.466:J:420:PRO:HA 6:J:437:PHE:O 2.15 0.466:J:847:ASP:OD1 6:J:847:ASP:N 2.49 0.467:K:25:ARG:NH2 7:K:65:ASP:OD1 2.44 0.465:I:1119:MET:HG3 5:I:1204:LEU:HD13 1.97 0.465:I:870:ILE:HB 5:I:944:ARG:HD3 1.98 0.465:I:735:LYS:HA 5:I:748:ILE:HG22 1.97 0.465:I:800:MET:HE3 5:I:800:MET:HB2 1.85 0.465:I:243:PRO:HB2 5:I:274:ILE:HG23 1.96 0.464:H:62:ASP:OD2 4:H:141:SER:HB3 2.16 0.465:I:93:SER:HA 5:I:128:PRO:HA 1.97 0.46





Clashoverlap (Å)

4:G:45:ARG:HH22 5:I:1216:ARG:HA 1.80 0.466:J:1219:ASP:O 6:J:1223:LEU:HB2 2.16 0.46

5:I:829:THR:HG23 5:I:1059:ARG:HA 1.97 0.465:I:1244:HIS:NE2 5:I:1266:GLY:O 2.35 0.455:I:1314:GLN:CB 7:K:28:ARG:HH12 2.22 0.455:I:1313:HIS:H 7:K:31:GLN:HE22 1.63 0.455:I:446:ASP:HA 5:I:451:ARG:HH21 1.81 0.456:J:50:LYS:NZ 6:J:71:LEU:O 2.31 0.455:I:588:GLU:HA 5:I:606:LEU:O 2.15 0.45

6:J:842:ARG:HH22 6:J:1250:ASP:HB2 1.80 0.456:J:43:THR:OG1 6:J:44:ILE:N 2.50 0.455:I:538:LEU:HD11 5:I:571:LEU:HD22 1.97 0.456:J:926:PRO:HB2 6:J:1241:TYR:HE1 1.82 0.456:J:515:ARG:NH2 6:J:718:SER:O 2.48 0.454:H:15:ASP:OD1 4:H:27:THR:OG1 2.28 0.455:I:855:PRO:HG3 5:I:913:VAL:HG13 1.98 0.454:H:99:ILE:HD11 4:H:143:ARG:HB3 1.98 0.455:I:974:ARG:HD2 5:I:1014:LEU:HD21 1.98 0.456:J:1108:GLN:HG3 6:J:1109:LEU:HD12 1.99 0.454:H:185:TYR:HA 4:H:202:VAL:O 2.17 0.456:J:1158:GLU:HA 6:J:1223:LEU:HD21 1.99 0.454:H:151:GLY:HA2 4:H:178:SER:HB3 1.99 0.445:I:176:ILE:HD12 5:I:184:LEU:HD23 1.99 0.445:I:1268:GLN:HE22 6:J:352:ARG:HD2 1.81 0.446:J:1227:HIS:HA 6:J:1230:THR:HG22 1.99 0.446:J:978:ARG:HD3 6:J:999:TYR:H 1.83 0.44

1:A:9:DG:N2 8:D:70:ASN:O 2.50 0.446:J:1026:PRO:HB2 6:J:1028:ILE:HG23 2.00 0.446:J:1079:LYS:HD3 6:J:1098:GLN:HB3 2.00 0.444:G:64:VAL:HG11 4:G:78:ILE:HG21 1.99 0.445:I:596:ASP:N 5:I:596:ASP:OD1 2.49 0.44

6:J:1033:GLY:HA3 6:J:1081:VAL:O 2.18 0.445:I:587:LEU:HD23 5:I:587:LEU:HA 1.89 0.445:I:985:GLU:HB3 5:I:988:LYS:HB2 1.99 0.445:I:469:VAL:HA 5:I:472:GLU:HG2 2.00 0.446:J:850:LYS:HB3 6:J:855:ASP:HB2 1.99 0.444:G:52:PRO:HD2 4:G:219:ARG:HH11 1.83 0.445:I:488:MET:O 5:I:490:GLN:N 2.47 0.445:I:524:ILE:HB 5:I:712:SER:HB2 1.99 0.43

6:J:1167:LYS:HZ2 6:J:1170:LYS:HB2 1.83 0.436:J:1357:ILE:HG22 6:J:1359:ALA:H 1.83 0.43





Clashoverlap (Å)

6:J:506:VAL:HG23 6:J:628:GLY:HA3 1.99 0.434:H:155:ALA:N 4:H:174:ASP:OD1 2.50 0.435:I:46:GLN:HA 5:I:47:TYR:HA 1.77 0.43

6:J:1024:THR:HG23 6:J:1123:ARG:HA 2.00 0.431:A:20:DG:H1’ 1:A:21:DC:H5’ 2.01 0.43

4:G:45:ARG:HH12 4:H:37:HIS:HB2 1.83 0.435:I:717:VAL:HG22 5:I:782:VAL:HG12 2.00 0.434:H:102:LEU:HB3 4:H:142:MET:HG2 2.00 0.435:I:95:PRO:HB3 5:I:123:TYR:HE1 1.83 0.436:J:1321:SER:OG 6:J:1349:GLU:OE2 2.21 0.434:H:79:LEU:HD21 6:J:526:VAL:HG11 2.00 0.435:I:400:VAL:HG21 5:I:452:ARG:HE 1.84 0.436:J:824:PRO:HD3 6:J:835:LEU:HD12 2.00 0.436:J:894:VAL:HG22 6:J:1258:ARG:HH11 1.83 0.43

1:A:1:DG:H2” 1:A:2:DG:C8 2.53 0.435:I:562:GLU:OE1 5:I:662:SER:OG 2.31 0.434:H:212:ASP:OD1 4:H:212:ASP:N 2.52 0.435:I:1002:LEU:HD21 5:I:1007:LYS:HB2 2.00 0.435:I:803:ALA:HB2 5:I:1094:VAL:HG21 1.99 0.435:I:830:THR:HG22 5:I:1234:LYS:NZ 2.34 0.435:I:300:ASP:OD1 5:I:313:ALA:N 2.52 0.435:I:623:LEU:HD13 5:I:627:GLY:HA2 2.01 0.436:J:1046:ILE:HG22 6:J:1061:VAL:HA 2.00 0.436:J:515:ARG:HH12 6:J:724:MET:HG2 1.83 0.436:J:417:ARG:NH1 7:K:43:ASN:O 2.52 0.431:A:10:DT:H6 1:A:10:DT:H2’ 1.63 0.422:B:21:DT:H5” 5:I:141:THR:HG21 2.01 0.427:K:50:ALA:O 7:K:54:ILE:HG12 2.19 0.425:I:796:LEU:N 5:I:1231:TYR:OH 2.52 0.425:I:55:SER:CB 5:I:465:ARG:HH12 2.32 0.42

6:J:246:PRO:HD2 6:J:249:LEU:HD12 2.01 0.425:I:1117:LEU:HD12 5:I:1195:ILE:HG12 2.00 0.425:I:395:TYR:HE2 5:I:420:LEU:HG 1.84 0.426:J:126:LEU:HD12 6:J:223:LEU:HD22 2.01 0.426:J:1350:ASN:HA 6:J:1353:VAL:HG12 2.02 0.426:J:140:TYR:OH 6:J:312:ARG:NE 2.53 0.426:J:559:ALA:HB3 6:J:562:GLU:HB3 2.01 0.424:H:188:GLU:OE2 4:H:200:LYS:HD3 2.19 0.425:I:1041:ASP:OD1 5:I:1041:ASP:N 2.52 0.425:I:529:ARG:HH22 5:I:687:ARG:HH11 1.66 0.424:G:44:ARG:HG3 4:G:183:ILE:HB 2.02 0.42





Clashoverlap (Å)

6:J:950:ILE:HB 6:J:1018:ALA:HB3 2.01 0.426:J:513:MET:HG3 6:J:544:LEU:HD11 2.01 0.425:I:934:PHE:HD1 5:I:1040:ASP:OD2 2.02 0.425:I:1102:GLY:HA2 5:I:1106:ARG:HH11 1.85 0.425:I:180:ARG:NH1 5:I:393:ASP:O 2.37 0.425:I:75:LEU:HD23 5:I:94:ALA:HB3 2.00 0.426:J:568:SER:HB3 6:J:570:LYS:NZ 2.34 0.426:J:820:ILE:HG12 6:J:884:SER:HB2 2.02 0.421:A:16:DG:OP1 5:I:175:ARG:NH2 2.52 0.422:B:24:DC:H6 2:B:24:DC:H2’ 1.69 0.42

6:J:364:HIS:HB2 6:J:485:MET:HE2 2.01 0.426:J:609:TYR:HD2 6:J:610:ARG:NH1 2.17 0.426:J:647:PRO:HG3 6:J:697:MET:HB3 2.01 0.428:D:16:ARG:NH1 8:D:73:ARG:HB3 2.35 0.424:H:35:PHE:HA 4:H:38:THR:HG22 2.01 0.425:I:230:PHE:HB2 5:I:333:ILE:HB 2.01 0.425:I:565:GLU:HA 5:I:569:ILE:HG12 2.01 0.425:I:68:LEU:HD11 5:I:100:LEU:HB3 2.01 0.426:J:1272:SER:OG 6:J:1273:ASP:N 2.53 0.425:I:593:LYS:HB3 5:I:602:GLU:HG3 2.02 0.425:I:972:PHE:HD1 5:I:975:ILE:HD12 1.85 0.426:J:930:LEU:HA 6:J:1244:GLN:HG3 2.02 0.426:J:1289:ASN:O 6:J:1293:GLU:HB2 2.20 0.41

4:G:182:ARG:NH1 5:I:1090:ASN:O 2.54 0.415:I:241:LEU:N 5:I:283:LYS:O 2.51 0.41

6:J:616:PRO:HA 6:J:619:ILE:HG22 2.02 0.418:D:65:HIS:CD2 8:D:67:THR:H 2.39 0.41

5:I:1042:LEU:HD22 5:I:1049:ILE:HD12 2.02 0.415:I:257:ALA:HB2 5:I:285:ILE:HG22 2.02 0.416:J:201:LEU:HB2 6:J:221:ILE:HD13 2.01 0.416:J:515:ARG:HG2 6:J:516:ASP:H 1.85 0.416:J:576:ARG:HD3 6:J:593:ASN:HA 2.03 0.415:I:666:SER:HB2 5:I:1186:VAL:HG21 2.00 0.415:I:211:ARG:HH21 5:I:351:LEU:HD22 1.86 0.416:J:137:ARG:HG2 6:J:142:GLU:OE2 2.20 0.418:D:4:TRP:CE2 8:D:93:ILE:HG21 2.56 0.41

4:G:190:ALA:HB2 4:G:200:LYS:HB2 2.01 0.415:I:104:ILE:HD11 5:I:116:ASP:HB2 2.02 0.415:I:56:VAL:HG11 5:I:468:LEU:HD13 2.03 0.416:J:291:ILE:HG23 8:D:54:TYR:CE2 2.55 0.416:J:848:VAL:HB 6:J:858:VAL:HG22 2.02 0.41





Clashoverlap (Å)

4:H:91:ARG:HG2 4:H:122:GLU:HB3 2.01 0.415:I:218:GLU:HG2 5:I:299:LYS:HA 2.02 0.414:G:231:PHE:HE1 4:H:28:LEU:HD11 1.85 0.415:I:812:PHE:HZ 6:J:503:SER:HB2 1.85 0.415:I:363:LEU:HA 5:I:363:LEU:HD23 1.90 0.415:I:69:GLN:HE21 5:I:101:ARG:HD2 1.85 0.416:J:1106:ILE:O 6:J:1123:ARG:N 2.46 0.416:J:230:SER:OG 6:J:231:GLY:N 2.53 0.413:R:14:A:H2’ 3:R:15:G:C8 2.56 0.41

5:I:1286:THR:O 5:I:1290:MET:HB2 2.21 0.416:J:586:GLY:HA3 6:J:612:LEU:HD11 2.01 0.416:J:797:THR:HG22 6:J:924:GLY:HA3 2.01 0.415:I:221:LEU:HD23 5:I:221:LEU:HA 1.93 0.41

5:I:302:ILE:O 5:I:330:HIS:NE2 2.34 0.416:J:805:GLN:HG3 6:J:1348:LYS:HD3 2.03 0.415:I:1105:SER:OG 6:J:731:ARG:NH2 2.54 0.415:I:1072:ASN:N 5:I:1072:ASN:OD1 2.47 0.40

6:J:1050:THR:HG23 6:J:1057:SER:HB3 2.03 0.404:H:19:VAL:HG12 4:H:20:SER:H 1.86 0.406:J:97:VAL:HG12 6:J:101:ARG:HG3 2.03 0.406:J:114:ILE:HD12 6:J:304:ASP:HB3 2.03 0.406:J:393:THR:OG1 6:J:394:ILE:N 2.55 0.406:J:605:LEU:HA 6:J:605:LEU:HD23 1.93 0.40

6:J:279:LEU:HD13 6:J:299:LEU:HD13 2.02 0.404:H:197:ASP:N 4:H:197:ASP:OD1 2.55 0.40

6:J:1223:LEU:HA 6:J:1223:LEU:HD23 1.89 0.406:J:224:LEU:HD23 6:J:224:LEU:HA 1.91 0.406:J:515:ARG:HH21 6:J:717:VAL:HG23 1.87 0.406:J:839:VAL:HG12 6:J:864:LEU:HD12 2.02 0.404:G:195:ARG:HE 4:G:198:LEU:HD11 1.86 0.404:H:89:ALA:HB1 4:H:210:THR:HG23 2.04 0.405:I:452:ARG:NH1 5:I:458:GLU:OE2 2.52 0.405:I:678:ARG:HD3 5:I:678:ARG:HA 1.88 0.405:I:6:THR:HA 5:I:9:LYS:HG3 2.03 0.40

5:I:942:ASP:OD1 5:I:942:ASP:N 2.54 0.406:J:351:GLY:O 6:J:467:ALA:HA 2.22 0.406:J:907:HIS:ND1 6:J:908:ILE:O 2.53 0.40

There are no symmetry-related clashes.


5.3 Torsion angles i○

5.3.1 Protein backbone i○

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

4 G 217/239 (91%) 197 (91%) 19 (9%) 1 (0%) 29 68

4 H 215/239 (90%) 202 (94%) 13 (6%) 0 100 100

5 I 1315/1342 (98%) 1204 (92%) 106 (8%) 5 (0%) 34 72

6 J 1329/1407 (94%) 1216 (92%) 111 (8%) 2 (0%) 47 81

7 K 81/91 (89%) 74 (91%) 7 (9%) 0 100 100

8 D 81/162 (50%) 74 (91%) 5 (6%) 2 (2%) 5 34

All All 3238/3480 (93%) 2967 (92%) 261 (8%) 10 (0%) 44 75

All (10) Ramachandran outliers are listed below:

Mol Chain Res Type5 I 596 ASP5 I 1158 LYS6 J 805 GLN8 D 53 ASN6 J 904 ALA8 D 52 PRO4 G 119 GLY5 I 697 LYS5 I 1159 VAL5 I 1317 PRO

5.3.2 Protein sidechains i○

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#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

4 G 186/206 (90%) 186 (100%) 0 100 100

4 H 187/206 (91%) 186 (100%) 1 (0%) 88 94

5 I 1138/1157 (98%) 1135 (100%) 3 (0%) 92 97

6 J 1120/1168 (96%) 1113 (99%) 7 (1%) 86 94

7 K 70/75 (93%) 70 (100%) 0 100 100

8 D 75/142 (53%) 75 (100%) 0 100 100

All All 2776/2954 (94%) 2765 (100%) 11 (0%) 91 96

All (11) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type4 H 12 ARG5 I 817 LEU5 I 1151 LEU5 I 1159 VAL6 J 53 ARG6 J 60 ARG6 J 514 THR6 J 709 ARG6 J 836 ARG6 J 1268 ASN6 J 1373 ARG

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (23)such sidechains are listed below:

Mol Chain Res Type4 H 41 ASN4 H 84 ASN5 I 150 HIS5 I 604 HIS5 I 760 ASN5 I 1116 HIS5 I 1157 GLN5 I 1236 ASN5 I 1268 GLN6 J 424 ASN6 J 450 HIS6 J 665 GLN6 J 777 HIS6 J 805 GLN



Continued from previous page...Mol Chain Res Type6 J 1108 GLN6 J 1235 ASN6 J 1268 ASN6 J 1279 GLN6 J 1326 GLN6 J 1350 ASN7 K 31 GLN8 D 20 HIS8 D 77 HIS

5.3.3 RNA i○

Mol Chain Analysed Backbone Outliers Pucker Outliers3 R 9/20 (45%) 0 0

There are no RNA backbone outliers to report.

There are no RNA pucker outliers to report.

5.4 Non-standard residues in protein, DNA, RNA chains i○

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

5.5 Carbohydrates i○

There are no monosaccharides in this entry.

5.6 Ligand geometry i○

Of 3 ligands modelled in this entry, 3 are 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.

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

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




5.7 Other polymers i○

There are no such residues in this entry.

5.8 Polymer linkage issues i○

There are no chain breaks in this entry.


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


6 Map visualisation i○

This section contains visualisations of the EMDB entry EMD-7350. These allow visual inspectionof the internal detail of the map and identification 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 i○

6.1.1 Primary map

X Y Z

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

6.2 Central slices i○

6.2.1 Primary map

X Index: 128 Y Index: 128 Z Index: 128

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


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

6.3 Largest variance slices i○

6.3.1 Primary map

X Index: 120 Y Index: 122 Z Index: 142

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

6.4 Orthogonal surface views i○

6.4.1 Primary map

X Y Z

The images above show the 3D surface view of the map at the recommended contour level 0.016.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_slices

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


6.5 Mask visualisation i○

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

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


7 Map analysis i○

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

7.1 Map-value distribution i○

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 i○

The volume at the recommended contour level is 269 nm3; this corresponds to an approximatemass of 243 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 i○

*Reported resolution corresponds to spatial frequency of 0.286 Å−1

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


8 Fourier-Shell correlation i○

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

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


9 Map-model fit i○

This section contains information regarding the fit between EMDB map EMD-7350 and PDBmodel 6C6T. Per-residue inclusion information can be found in section 3 on page 6.

9.1 Map-model overlay i○

X Y Z

The images above show the 3D surface view of the map at the recommended contour level 0.016at 50% 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 fit 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 i○

At the recommended contour level, 87% of all backbone atoms, 83% of all non-hydrogen atoms,are inside the map.

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

full wwpdb em validation report i - rcsb · 2020. 12. 13. · page5 fullwwpdbemvalidationreport...

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