full wwpdb em map/model validation report o i · page 4 ullf wwpdb em map/model alidationv report...

Full wwPDB EM Validation Report i○

Dec 15, 2020 – 03:54 PM EST

PDB ID : 6NE3EMDB ID : EMD-9356

Title : Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2hbound at SHL-2

Authors : Armache, J.-P.; Gamarra, N.; Johnson, S.L.; Leonard, J.D.; Wu, S.; Narlikar,G.N.; Cheng, Y.

Deposited on : 2018-12-16Resolution : 3.90 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.dev61Mogul : 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) : 2.15.1

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



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

Full wwPDB EM Validation Report EMD-9356, 6NE3

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 3.90 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 3826

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 136

1 E 136

2 B 103

2 F 103

3 C 130

3 G 130

4 D 99

5 H 93Continued on next page...

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


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

6 J 156

7 I 156

8 W 467


2 Entry composition i○

There are 9 unique types of molecules in this entry. The entry contains 16336 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 Histone H3.2.

Mol Chain Residues Atoms AltConf Trace

1 A 99 Total C N O S806 509 154 140 3 0 0

1 E 99 Total C N O S813 512 157 141 3 0 0

There are 2 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 102 ALA GLY engineered mutation UNP P84233E 102 ALA GLY engineered mutation UNP P84233

• Molecule 2 is a protein called Histone H4.


2 B 88 Total C N O S704 442 142 119 1 0 0

2 F 83 Total C N O S652 412 125 114 1 0 0

• Molecule 3 is a protein called Histone H2A type 1.


3 C 114 Total C N O867 545 169 153 0 0

3 G 109 Total C N O831 522 164 145 0 0

There are 2 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceC 99 ARG GLY engineered mutation UNP P06897G 99 ARG GLY engineered mutation UNP P06897

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


• Molecule 4 is a protein called Histone H2B.


4 D 99 Total C N O S780 490 145 143 2 0 0

• Molecule 5 is a protein called Histone H2B.


5 H 93 Total C N O S726 457 130 137 2 0 0

• Molecule 6 is a DNA chain called DNA (156-MER).


6 J 156 Total C N O P3178 1512 573 938 155 0 0

• Molecule 7 is a DNA chain called DNA (156-MER).


7 I 156 Total C N O P3215 1522 605 932 156 0 0

• Molecule 8 is a protein called SWI/SNF-related matrix-associated actin-dependent regulatorof chromatin subfamily A member 5.


8 W 461 Total C N O S3737 2388 655 670 24 0 0

• Molecule 9 is ADENOSINE-5’-DIPHOSPHATE (three-letter code: ADP) (formula:C10H15N5O10P2).


Mol Chain Residues Atoms AltConf

9 W 1 Total C N O P27 10 5 10 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: Histone H3.2

Chain A:

MET

ALA

ARG

THR

LYS

GLN

THR

ALA

ARG

LYS

SER

THR

GLY

GLY

LYS

ALA

PRO

ARG

LYS

GLN

LEU

ALA

THR

LYS

ALA

ALA

ARG

LYS

SER

ALA

PRO

ALA

THR

GLY

GLY

VAL

K36

R63

Q68

R69

R72

T80

D81

L82

R83

F84

Q85

V89

L92

S96

R116

I119

D123

A127

R131

R134

ALA

• Molecule 1: Histone H3.2

Chain E:

MET

ALA

ARG

THR

LYS

GLN

THR

ALA

ARG

LYS

SER

THR

GLY

GLY

LYS

ALA

PRO

ARG

LYS

GLN

LEU

ALA

THR

LYS

ALA

ALA

ARG

LYS

SER

ALA

PRO

ALA

THR

GLY

GLY

VAL

LYS

K37

R40

Y41

R42

R49

L61

I62

R63

P66

R69

K79

T80

L92

Q93

E97

L100

L103

D106

R116

V117

T118

I119

M120

D123

R131

R134

�A1

35�

• Molecule 2: Histone H4

Chain B:

MET

SER

GLY

ARG

GLY

LYS

GLY

GLY

LYS

GLY

LEU

GLY

LYS

GLY

GLY

A15

N25

R35

R39

K44

R45

I46

Y51

L58

R78

T82

D85

G102

�

• Molecule 2: Histone H4

Chain F:

MET

SER

GLY

ARG

GLY

LYS

GLY

GLY

LYS

GLY

LEU

GLY

LYS

GLY

GLY

ALA

LYS

ARG

HIS

ARG

K20

V21

�

I34

R35

R36

L37

A38

R39

K44

R45

R55

L62

V65

I66

H75

A76

K77

G102

�

• Molecule 3: Histone H2A type 1

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


Chain C:ME

TSE

RGL

YAR

GGL

YLY

SGL

NGL

YG8

�K9 T1

0�

P26

R29

R35

R42

V43

G44

L55

I79

P80

R81

Q84

V87

L97

I102

K119

�T1

20�

E121

�SE

RAL

ALY

SSE

RAL

ALY

SSE

RLY

S

• Molecule 3: Histone H2A type 1

Chain G:

MET

SER

GLY

ARG

GLY

LYS

GLN

GLY

GLY

LYS

THR

R11

T16

R17

S18

S19

R20

R29

V30

H31

R35

V54

L55

R71

K74

K75

T76

R77

L85

A86

V87

R88

N89

L93

L97

V100

K119

THR

GLU

SER

ALA

LYS

SER

ALA

LYS

SER

LYS

• Molecule 4: Histone H2B

Chain D:

K24

�K2

5

E32

D65

V66

F67

L77

N81

K82

R83

S84

T85

I86

T87

S88

R89

E90

L103

K122

• Molecule 5: Histone H2B

Chain H:

T29

R30

Y37

D48

D65

V66

F67

E68

R69

L77

N81

T87

S88

R89

E90

T93

L99

A104

A107

A121

• Molecule 6: DNA (156-MER)

Chain J:

C0 T1 G2 A6 A7 A19

G20

G36

T37

A38

G39

A40

G49

C52

A59

A60

C61

G84

C91

C92

A96

T111

A112

A132

T133

A134

C142

C143

T144

G145

G151

�T1

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A153

�T1

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T155

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• Molecule 7: DNA (156-MER)

Chain I:

A52

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�A5

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C60

A61

G98

G99

A100

G101

T102

G112

A119

G128

G129

C135

G136

T149

G154

T169

A170

C171

T179

G180

A181

G185

C186

C187

T188

T203

G207

• Molecule 8: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin sub-family A member 5

Chain W:

T166

R167

F168

E169

�D1

70�

K179

L180

R181

Q184

V185

R186

N189

W190

L191

I192

S193

L194

N200

M207

G208

L209

G210

K211

T212

L213

Q214

L219

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V234

L235

V236

S239

T240

L241

H242

R250

W251

V258

C259

L260

I261

R267

F270

V271

R272

L275

L276

P277


G278

E279

V284

M289

N301

W302

R303

V306

I307

D308

H311

R312

I313

K314

N315

E316

L320

I323

K328

T329

T330

N331

R332

L333

L334

L335

T336

G337

T338

P339

L340

Q341

N342

N343

�L3

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45

W348

S349

D357

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N360

�

D363

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F369

ASP

THR

ASN

CYS

LEU

GLY

Q378

�K3

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L380

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L384

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R394

R395

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D475

M476

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S482

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G499

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Q507

L512

M520

W521

R522

N523

Y524

E525

R528

�L5

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30G5

31Q5

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H535

R538

Q539

D540

N549

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K552

R560

L564

G565

I566

N567

L568

A569

D572

D580

P583

Q584

V585

D586

L587

M590

D591

R592

R595

Q598

T601

V602

R603

V604

F607

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T609

T612

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A621

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4 Experimental information i○

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, Not providedNumber of particles used 27513 DepositorResolution determination method FSC 0.143 CUT-OFF DepositorCTF correction method PHASE FLIPPING AND AMPLITUDE

CORRECTIONDepositor

Microscope FEI POLARA 300 DepositorVoltage (kV) 300 DepositorElectron dose (e−/Å2

) 41 DepositorMinimum defocus (nm) Not providedMaximum defocus (nm) Not providedMagnification Not providedImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 2.053 DepositorMinimum map value -1.175 DepositorAverage map value 0.001 DepositorMap value standard deviation 0.072 DepositorRecommended contour level 0.245 DepositorMap size (Å) 364.68, 364.68, 364.68 wwPDBMap dimensions 300, 300, 300 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.2156, 1.2156, 1.2156 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:ADP

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 0.42 0/818 0.59 1/1100 (0.1%)1 E 0.44 0/825 0.55 0/11072 B 0.45 0/712 0.58 0/9512 F 0.46 0/659 0.60 1/883 (0.1%)3 C 0.39 0/877 0.55 0/11833 G 0.42 0/841 0.55 0/11374 D 0.41 0/791 0.51 0/10615 H 0.42 0/737 0.51 0/9936 J 0.96 0/3560 1.07 2/5489 (0.0%)7 I 0.95 0/3611 1.02 1/5575 (0.0%)8 W 0.31 0/3818 0.57 2/5162 (0.0%)All All 0.68 0/17249 0.81 7/24641 (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 outliers8 W 0 2

There are no bond length outliers.

All (7) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)7 I 185 DG O4’-C4’-C3’ -7.61 101.43 106.006 J 49 DG O4’-C4’-C3’ -6.27 101.99 104.502 F 62 LEU CA-CB-CG 6.17 129.50 115.301 A 92 LEU CA-CB-CG 5.95 128.99 115.308 W 435 LEU CA-CB-CG 5.47 127.89 115.30

Continued on next page...

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)8 W 344 LEU CA-CB-CG 5.46 127.86 115.306 J 2 DG P-O3’-C3’ 5.23 125.97 119.70

There are no chirality outliers.

All (2) planarity outliers are listed below:

Mol Chain Res Type Group8 W 469 GLY Peptide8 W 470 PRO 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 806 0 833 15 01 E 813 0 847 18 02 B 704 0 749 7 02 F 652 0 687 9 03 C 867 0 917 9 03 G 831 0 875 13 04 D 780 0 814 9 05 H 726 0 747 11 06 J 3178 0 1755 16 07 I 3215 0 1750 19 08 W 3737 0 3736 85 09 W 27 0 10 3 0All All 16336 0 13720 179 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 6.

All (179) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:A:127:ALA:O 1:A:131:ARG:HB2 1.87 0.74Continued on next page...

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


Continued from previous page...


Clashoverlap (Å)

3:G:85:LEU:O 3:G:89:ASN:HB2 1.90 0.728:W:426:ARG:HB3 8:W:432:ILE:HD13 1.80 0.648:W:207:MET:O 8:W:397:LYS:NZ 2.32 0.62

8:W:260:LEU:HD11 8:W:267:ARG:HG2 1.80 0.621:E:116:ARG:NH1 1:E:120:MET:SD 2.73 0.621:E:40:ARG:NH2 6:J:84:DG:N3 2.48 0.611:A:69:ARG:HB3 2:B:25:ASN:HD21 1.65 0.611:E:118:THR:OG1 2:F:45:ARG:NH1 2.34 0.608:W:528:ARG:HE 8:W:530:ASP:HB3 1.66 0.603:C:87:VAL:HG21 3:C:97:LEU:HD22 1.84 0.608:W:341:GLN:HA 8:W:584:GLN:HE22 1.67 0.603:C:55:LEU:HD21 4:D:67:PHE:HB2 1.83 0.598:W:529:LEU:HD11 8:W:538:ARG:HG3 1.85 0.598:W:409:GLU:HA 8:W:604:VAL:HB 1.85 0.591:A:116:ARG:NH2 1:A:123:ASP:OD2 2.36 0.581:E:62:ILE:HG23 1:E:93:GLN:HE21 1.68 0.588:W:427:ILE:HG13 8:W:445:ARG:HE 1.69 0.588:W:525:GLU:HB2 8:W:552:LYS:HA 1.87 0.578:W:301:ASN:OD1 8:W:328:LYS:NZ 2.38 0.571:A:85:GLN:HE21 2:B:82:THR:HA 1.70 0.571:A:63:ARG:HH21 6:J:61:DC:H4’ 1.70 0.578:W:507:GLN:NE2 8:W:580:ASP:OD2 2.37 0.571:A:83:ARG:HG2 8:W:447:LEU:HD21 1.87 0.573:G:75:LYS:NZ 6:J:134:DA:OP2 2.38 0.565:H:65:ASP:OD2 5:H:69:ARG:NH2 2.38 0.567:I:154:DG:H3’ 8:W:314:LYS:HE2 1.87 0.56

1:E:116:ARG:HH12 1:E:120:MET:HB2 1.70 0.562:F:39:ARG:NH1 2:F:44:LYS:O 2.39 0.562:F:62:LEU:HA 2:F:65:VAL:HG12 1.88 0.564:D:77:LEU:O 4:D:81:ASN:ND2 2.39 0.555:H:77:LEU:O 5:H:81:ASN:ND2 2.38 0.55

1:E:42:ARG:NH2 7:I:203:DT:OP2 2.39 0.558:W:330:THR:OG1 8:W:331:ASN:ND2 2.39 0.555:H:29:THR:OG1 5:H:30:ARG:N 2.40 0.551:E:79:LYS:NZ 1:E:80:THR:O 2.39 0.541:E:66:PRO:HA 1:E:69:ARG:HE 1.72 0.54

8:W:384:LEU:HD21 8:W:634:GLN:HB3 1.90 0.543:C:26:PRO:HB2 3:C:29:ARG:HB3 1.89 0.548:W:540:ASP:N 8:W:540:ASP:OD1 2.41 0.54

3:G:87:VAL:HG21 3:G:97:LEU:HD12 1.89 0.538:W:612:THR:HG23 8:W:614:GLU:H 1.74 0.53





Clashoverlap (Å)

8:W:629:SER:HA 8:W:632:ILE:HG22 1.89 0.538:W:560:ARG:O 8:W:564:LEU:HB2 2.08 0.538:W:566:ILE:O 8:W:592:ARG:NH1 2.41 0.538:W:345:HIS:HA 8:W:348:TRP:HB3 1.90 0.535:H:87:THR:N 5:H:90:GLU:OE1 2.40 0.53

1:A:63:ARG:NH1 7:I:149:DT:O3’ 2.43 0.528:W:239:SER:OG 8:W:538:ARG:NH1 2.42 0.528:W:211:LYS:HB3 8:W:335:LEU:HD11 1.92 0.523:G:88:ARG:NH2 3:G:100:VAL:O 2.41 0.523:G:71:ARG:O 3:G:74:LYS:NZ 2.43 0.526:J:59:DA:OP1 8:W:267:ARG:NH2 2.40 0.52

8:W:242:HIS:HE1 8:W:535:HIS:HB2 1.75 0.518:W:530:ASP:OD2 8:W:532:GLN:NE2 2.43 0.512:B:35:ARG:NH2 2:B:51:TYR:OH 2.43 0.512:F:35:ARG:HH21 2:F:39:ARG:HH21 1.58 0.512:B:78:ARG:NH2 2:B:85:ASP:OD2 2.43 0.518:W:185:VAL:O 8:W:189:ASN:ND2 2.44 0.518:W:191:LEU:HA 8:W:194:LEU:HD12 1.92 0.518:W:340:LEU:O 8:W:584:GLN:NE2 2.43 0.511:E:103:LEU:HA 1:E:131:ARG:HH22 1.75 0.518:W:572:ASP:OD2 8:W:603:ARG:NH2 2.44 0.513:C:35:ARG:NH2 7:I:171:DC:OP2 2.39 0.518:W:444:MET:O 8:W:452:GLN:NE2 2.44 0.503:C:84:GLN:HB2 3:C:102:ILE:HD11 1.93 0.506:J:6:DA:H2” 6:J:7:DA:H2’ 1.92 0.50

8:W:186:ARG:HA 8:W:189:ASN:HD22 1.75 0.508:W:512:LEU:HD21 8:W:528:ARG:HG3 1.94 0.503:G:29:ARG:NH2 5:H:37:TYR:OH 2.45 0.498:W:411:LYS:HE2 8:W:608:ILE:HG21 1.93 0.492:F:34:ILE:HD11 2:F:55:ARG:HE 1.76 0.49

8:W:271:VAL:HG23 8:W:275:LEU:HB2 1.93 0.491:A:119:ILE:HD11 2:B:46:ILE:HG23 1.94 0.494:D:32:GLU:HA 7:I:181:DA:H5” 1.95 0.491:A:96:SER:HB2 2:B:58:LEU:HD11 1.94 0.493:C:44:GLY:HA2 7:I:170:DA:H5” 1.96 0.488:W:210:GLY:O 8:W:214:GLN:N 2.47 0.48

8:W:405:PRO:HG2 8:W:601:THR:HA 1.95 0.488:W:477:HIS:O 8:W:481:ASN:ND2 2.46 0.485:H:48:ASP:OD1 5:H:48:ASP:N 2.45 0.488:W:396:ILE:HG23 8:W:398:ALA:H 1.77 0.488:W:614:GLU:HA 8:W:617:ILE:HD12 1.95 0.48





Clashoverlap (Å)

3:C:29:ARG:NH2 7:I:181:DA:OP1 2.47 0.483:C:79:ILE:HG13 3:C:81:ARG:H 1.78 0.488:W:277:PRO:HG2 8:W:279:GLU:HB2 1.95 0.488:W:476:MET:SD 8:W:522:ARG:NH2 2.73 0.488:W:569:ALA:O 8:W:598:GLN:NE2 2.40 0.481:E:63:ARG:NH1 7:I:119:DA:OP1 2.47 0.476:J:144:DT:H1’ 6:J:145:DG:H5’ 1.96 0.47

8:W:306:VAL:HG22 8:W:333:LEU:HB2 1.95 0.478:W:312:ARG:HG2 8:W:320:LEU:HD13 1.95 0.473:G:77:ARG:HH21 6:J:132:DA:H4’ 1.79 0.478:W:181:ARG:N 8:W:184:GLN:OE1 2.46 0.47

8:W:267:ARG:NH1 8:W:289:MET:SD 2.85 0.478:W:522:ARG:HD3 8:W:522:ARG:HA 1.68 0.473:C:42:ARG:HG3 4:D:85:THR:HG23 1.97 0.478:W:311:HIS:NE2 8:W:338:THR:O 2.49 0.466:J:39:DG:N2 7:I:169:DT:O2 2.48 0.46

3:G:55:LEU:HD11 5:H:67:PHE:HB2 1.96 0.468:W:167:ARG:HD2 8:W:192:ILE:HG21 1.96 0.468:W:213:LEU:HD11 8:W:251:TRP:CD2 2.51 0.463:G:87:VAL:HG23 3:G:93:LEU:HB3 1.98 0.468:W:520:MET:O 8:W:523:ASN:ND2 2.48 0.467:I:179:DT:H2” 7:I:180:DG:C8 2.51 0.46

8:W:450:LEU:HB2 8:W:613:VAL:HG11 1.98 0.462:B:39:ARG:NH1 2:B:44:LYS:O 2.46 0.451:E:97:GLU:HG2 2:F:37:LEU:HD21 1.97 0.452:F:75:HIS:HB2 5:H:93:THR:HG21 1.98 0.45

8:W:414:VAL:HG11 8:W:484:LYS:HA 1.98 0.451:E:106:ASP:OD2 1:E:131:ARG:NH2 2.50 0.451:E:120:MET:N 1:E:123:ASP:OD2 2.49 0.452:F:77:LYS:HG3 5:H:89:ARG:HH22 1.82 0.456:J:36:DG:H2” 6:J:37:DT:H5” 1.99 0.452:F:66:ILE:HA 2:F:66:ILE:HD13 1.85 0.45

1:E:116:ARG:NH2 1:E:123:ASP:OD1 2.50 0.458:W:420:GLN:HE21 8:W:482:SER:HB3 1.81 0.458:W:583:PRO:HB3 8:W:621:ALA:HB1 1.99 0.453:G:17:ARG:HG2 3:G:20:ARG:HH21 1.82 0.443:G:54:VAL:HG13 5:H:107:ALA:HB1 2.00 0.441:A:68:GLN:HE21 1:A:72:ARG:HH21 1.66 0.448:W:303:ARG:O 8:W:330:THR:OG1 2.31 0.44

8:W:595:ARG:NH1 9:W:801:ADP:O2A 2.49 0.444:D:87:THR:N 4:D:90:GLU:OE1 2.39 0.43





Clashoverlap (Å)

3:G:16:THR:O 3:G:19:SER:OG 2.30 0.438:W:567:ASN:OD1 8:W:567:ASN:N 2.51 0.438:W:484:LYS:HE3 8:W:609:THR:HG23 1.99 0.435:H:99:LEU:HB2 5:H:104:ALA:HB2 2.00 0.436:J:39:DG:H1’ 6:J:40:DA:C5 2.53 0.43

8:W:250:ARG:HD2 8:W:250:ARG:HA 1.88 0.438:W:338:THR:OG1 8:W:338:THR:O 2.31 0.431:E:100:LEU:HD23 1:E:100:LEU:HA 1.87 0.438:W:584:GLN:HA 8:W:587:LEU:HD12 2.00 0.438:W:179:LYS:H 8:W:251:TRP:HZ3 1.65 0.43

8:W:469:GLY:HA2 8:W:470:PRO:HD3 1.86 0.433:G:31:HIS:CD2 3:G:35:ARG:HE 2.36 0.426:J:96:DA:N6 7:I:112:DG:O6 2.52 0.427:I:187:DC:H2” 7:I:188:DT:C5 2.55 0.421:A:127:ALA:O 1:A:131:ARG:CB 2.61 0.421:A:89:VAL:HA 1:A:92:LEU:HD23 2.01 0.426:J:111:DT:H2” 6:J:112:DA:C8 2.54 0.427:I:60:DC:H2” 7:I:61:DA:C8 2.55 0.428:W:337:GLY:O 8:W:394:ARG:NH1 2.53 0.42

8:W:166:THR:OG1 8:W:167:ARG:N 2.52 0.428:W:234:VAL:HB 8:W:284:VAL:HG12 2.02 0.426:J:91:DC:H1’ 6:J:92:DC:C5 2.55 0.42

8:W:272:ARG:HA 8:W:272:ARG:HD3 1.78 0.428:W:316:GLU:HB3 8:W:349:SER:HB2 2.02 0.428:W:443:LYS:HG2 8:W:446:LEU:HD22 2.00 0.428:W:475:ASP:N 8:W:475:ASP:OD1 2.53 0.428:W:586:ASP:O 8:W:590:MET:HB2 2.20 0.426:J:142:DC:H2” 6:J:143:DC:H5” 2.02 0.428:W:211:LYS:N 9:W:801:ADP:O1A 2.52 0.42

8:W:427:ILE:HD11 8:W:452:GLN:HB3 2.01 0.427:I:169:DT:H2’ 7:I:170:DA:C8 2.54 0.417:I:98:DG:H2” 7:I:99:DG:H8 1.85 0.41

4:D:87:THR:OG1 4:D:88:SER:N 2.50 0.411:E:61:LEU:N 1:E:97:GLU:OE2 2.51 0.41

8:W:208:GLY:HA2 9:W:801:ADP:H5’2 2.02 0.416:J:52:DC:H4’ 8:W:447:LEU:HB2 2.02 0.41

1:A:72:ARG:HD3 8:W:443:LYS:HE3 2.02 0.418:W:236:VAL:HG12 8:W:308:ASP:HB3 2.02 0.41

7:I:135:DC:H2” 7:I:136:DG:C8 2.56 0.416:J:19:DA:H1’ 6:J:20:DG:C5 2.54 0.41

4:D:24:LYS:HB3 4:D:25:LYS:H 1.53 0.41Continued on next page...




Clashoverlap (Å)

8:W:320:LEU:HA 8:W:323:ILE:HG22 2.03 0.418:W:311:HIS:CE1 8:W:336:THR:HG1 2.39 0.418:W:258:VAL:HB 8:W:270:PHE:HZ 1.84 0.411:E:92:LEU:HD23 1:E:92:LEU:HA 1.87 0.417:I:128:DG:H2” 7:I:129:DG:C8 2.56 0.41

8:W:200:ASN:OD1 8:W:332:ARG:N 2.48 0.418:W:484:LYS:HG2 8:W:607:PHE:HB3 2.02 0.411:A:63:ARG:HD3 7:I:149:DT:H4’ 2.02 0.414:D:103:LEU:HD12 4:D:103:LEU:HA 1.95 0.418:W:261:ILE:HA 8:W:261:ILE:HD12 1.91 0.401:A:80:THR:OG1 1:A:81:ASP:N 2.55 0.404:D:83:ARG:NH1 4:D:90:GLU:OE2 2.45 0.401:E:41:TYR:HE1 1:E:49:ARG:HH22 1.70 0.407:I:101:DG:H1’ 7:I:102:DT:H5’ 2.03 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

1 A 97/136 (71%) 92 (95%) 5 (5%) 0 100 100

1 E 97/136 (71%) 91 (94%) 6 (6%) 0 100 100

2 B 86/103 (84%) 80 (93%) 6 (7%) 0 100 100

2 F 81/103 (79%) 77 (95%) 4 (5%) 0 100 100

3 C 112/130 (86%) 106 (95%) 6 (5%) 0 100 100

3 G 107/130 (82%) 103 (96%) 4 (4%) 0 100 100

4 D 97/99 (98%) 89 (92%) 8 (8%) 0 100 100

5 H 91/93 (98%) 89 (98%) 2 (2%) 0 100 100

8 W 457/467 (98%) 413 (90%) 44 (10%) 0 100 100Continued on next page...

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

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


Continued from previous page...Mol Chain Analysed Favoured Allowed Outliers Percentiles

All All 1225/1397 (88%) 1140 (93%) 85 (7%) 0 100 100

There are no Ramachandran outliers to report.

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.

Mol Chain Analysed Rotameric Outliers Percentiles

1 A 84/111 (76%) 84 (100%) 0 100 100

1 E 85/111 (77%) 85 (100%) 0 100 100

2 B 71/79 (90%) 71 (100%) 0 100 100

2 F 66/79 (84%) 65 (98%) 1 (2%) 65 80

3 C 87/101 (86%) 87 (100%) 0 100 100

3 G 83/101 (82%) 83 (100%) 0 100 100

4 D 84/85 (99%) 83 (99%) 1 (1%) 71 83

5 H 79/79 (100%) 79 (100%) 0 100 100

8 W 408/429 (95%) 405 (99%) 3 (1%) 84 90

All All 1047/1175 (89%) 1042 (100%) 5 (0%) 89 93

All (5) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type4 D 65 ASP2 F 62 LEU8 W 240 THR8 W 332 ARG8 W 445 ARG

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (20)such sidechains are listed below:

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


Mol Chain Res Type1 A 39 HIS1 A 68 GLN1 A 85 GLN1 A 108 ASN2 B 25 ASN3 C 68 ASN3 C 104 GLN4 D 46 HIS4 D 81 ASN1 E 93 GLN2 F 25 ASN3 G 31 HIS5 H 60 ASN8 W 189 ASN8 W 242 HIS8 W 243 ASN8 W 331 ASN8 W 523 ASN8 W 543 ASN8 W 584 GLN

5.3.3 RNA i○

There are no RNA molecules in this entry.

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○

1 ligand is 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 defined in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bond

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

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




length (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 Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

9 ADP W 801 - 24,29,29 0.96 1 (4%) 29,45,45 1.54 4 (13%)

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 defined in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.’-’ means no outliers of that kind were identified.

Mol Type Chain Res Link Chirals Torsions Rings9 ADP W 801 - - 1/12/32/32 0/3/3/3

All (1) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)9 W 801 ADP C5-C4 2.50 1.47 1.40

All (4) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)9 W 801 ADP PA-O3A-PB -4.01 119.08 132.839 W 801 ADP C3’-C2’-C1’ 3.42 106.13 100.989 W 801 ADP N3-C2-N1 -3.17 123.72 128.689 W 801 ADP C4-C5-N7 -2.94 106.34 109.40

There are no chirality outliers.

All (1) torsion outliers are listed below:

Mol Chain Res Type Atoms9 W 801 ADP O4’-C4’-C5’-O5’

There are no ring outliers.

1 monomer is involved in 3 short contacts:

Mol Chain Res Type Clashes Symm-Clashes9 W 801 ADP 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. In


addition, 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 identified 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 identified 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-identified 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 find sufficientequivalents in the CSD to analyse the geometry.

Ligand ADP W 801

Bond lengths Bond angles

Torsions Rings

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-9356. 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: 150 Y Index: 150 Z Index: 150

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: 136 Y Index: 119 Z Index: 113

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 0.245.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 192 nm3; this corresponds to an approximatemass of 174 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 0.256 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-9356 and PDBmodel 6NE3. Per-residue inclusion information can be found in section 3 on page 7.

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 0.245at 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, 93% of all backbone atoms, 88% of all non-hydrogen atoms,are inside the map.

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

full wwpdb em map/model validation report o i · page 4 ullf wwpdb em map/model alidationv report...

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