Full wwPDB EM Validation Report i...X50 X51 X52 Page6 FullwwPDBEMValidationReport EMD-3245,3JC2 4...

Full wwPDB EM Validation Report i○

Dec 22, 2020 – 07:22 PM EST

PDB ID : 3JC2EMDB ID : EMD-3245

Title : The structure of the mammalian Sec61 channel opened by a signal sequenceAuthors : Voorhees, R.M.; Hegde, R.S.

Deposited on : 2015-11-15Resolution : 3.60 Å(reported)

Based on initial models : 1RH5, 3J7Q

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) : 2.16

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-3245, 3JC2

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 3.60 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 4297

Ramachandran outliers 154571 4023Sidechain 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


2 Entry composition i○

There are 4 unique types of molecules in this entry. The entry contains 3911 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 Protein transport protein Sec61 subunit alpha isoform 1.

Mol Chain Residues Atoms AltConf Trace

1 1 401 Total C N O S3115 2053 501 542 19 0 0

• Molecule 2 is a protein called Protein transport protein Sec61 subunit gamma.


2 2 62 Total C N O S494 326 86 79 3 0 0

• Molecule 3 is a protein called Prolactin.


3 w 19 Total C N O S142 94 24 23 1 0 0

• Molecule 4 is a protein called Protein transport protein Sec61 subunit beta.


4 3 32 Total C N O160 96 32 32 0 0

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


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: Protein transport protein Sec61 subunit alpha isoform 1

Chain 1:

MET

ALA

ILE

LYS

PHE

LEU

GLU

VAL

ILE

LYS

P11

�F1

2�

C13

�V1

4�

I15

�L1

6�

P17

�E1

8�

I19

�Q2

0�

K21

�P2

2�

E23

�R2

4�

K25

�I2

6�

Q27

�F2

8K2

9�

E30

K31

�V3

2L3

3�

W34

T35

�A3

6�

I37

T38

L39

�F4

0�

I41

�

V44

�C4

5�

C46

Q47

�I4

8�

P49

�L5

0�

F51

�G5

2�

I53

�ME

TSE

RSE

RAS

PSE

RAL

AAS

PPR

O

PHE

TYR

TRP

MET

ARG

VAL

ILE

LEU

ALA

SER

ASN

ARG

G74

T75

�L7

6�

M77

�E7

8�

L79

�G8

0�

I81

�S8

2�

V85

�T8

6S8

7G8

8�

L89

�I9

0�

M91

�Q9

2�

L93

�L9

4�

A95

�G9

6�

A97

�K9

8�

I99

�I1

00�

E101

�V1

02�

G103

�D1

04�

T105

�P1

06�

K107

�D1

08�

R109

�A1

10�

L111

�F1

12�

N113

�G1

14�

K117

�L1

18�

F119

�G1

20�

M121

�I1

22�

I123

T124

�

Q127

�S1

28I1

29�

V130

�Y1

31�

V132

�M1

33�

T134

G135

MET

TYR

GLY

ASP

PRO

SER

GLU

MET

GLY

ALA

GLY

I147

�C1

48�

L149

�L1

50�

I151

�T1

52�

I153

�Q1

54�

L155

�F1

56�

V157

�A1

58�

G159

�L1

60�

I161

�V1

62L1

63�

L164

�L1

65�

D166

�E1

67L1

68�

L169

�Q1

70�

K171

�G1

72Y1

73�

G174

�L1

75�

G176

�S1

77�

G178

I179

�

F182

�I1

83�

A184

�

I187

C188

�E1

89�

T190

I191

�V1

92W1

93�

K194

�A1

95F1

96S1

97�

P198

�T1

99�

T200

�V2

01�

N202

�T2

03�

G204

�R2

05�

G206

�M2

07�

E208

�F2

09�

E210

�G2

11A2

12�

I213

�I2

14�

A215

�L2

16�

F217

�H2

18�

L219

�L2

20�

A221

�T2

22�

R223

�T2

24�

D225

�K2

26�

V227

�R2

28�

A229

�L2

30�

R231

�E2

32�

A233

�F2

34�

Y235

�R2

36�

Q237

�N2

38�

L239

�P2

40N2

41L2

42M2

43�

N244

�L2

45�

I246

A247

�

F252

�A2

53�

V254

�V2

55I2

56

Q259

�G2

60F2

61R2

62V2

63D2

64L2

65P2

66I2

67K2

68S2

69A2

70R2

71Y2

72

Q275

Y276

N277

�T2

78Y2

79

K282

L283

F284

Y285

T286

S287

�N2

88�

I289

�P2

90I2

91�

I292

L293

�Q2

94�

S295

A296

�L2

97�

V298

�S2

99�

N300

�L3

01�

Y302

�V3

03�

I304

�S3

05�

Q306

�M3

07�

L308

�S3

09�

A310

�R3

11�

F312

�

SER

GLY

ASN

LEU

LEU

VAL

SER

LEU

LEU

GLY

THR

TRP

SER

ASP

THR

SER

SER

GLY

GLY

PRO

ALA

ARG

ALA

TYR

P337

�V3

38�

G339

�G3

40�

L341

�C3

42�

H343

�Y3

44�

L345

�S3

46�

P347

�P3

48�

E349

�S3

50�

F351

�G3

52�

S353

�V3

54�

L355

�E3

56�

D357

�P3

58�

V359

�H3

60�

A361

�V3

62�

V363

�Y3

64�

F367

�M3

68�

L369

�G3

70�

S371

�C3

72A3

73�

F374

�F3

75�

W379

I380

E381

�

S385

�S3

86A3

87K3

88D3

89

Q393

L394

K395

�E3

96�

M399

V400

M401

R402

G403

H404

R405

M409

V410

H411

E412

�L4

13N4

14R4

15Y4

16I4

17P4

18

L426

�C4

27I4

28�

G429

A430

�L4

31�

S432

V433

�L4

34�

A435

�D4

36�

F437

�L4

38�

G439

�A4

40I4

41�

G442

�S4

43�

G444

�

I447

L448

V451

T452

I453

I454

Y455

�Q4

56

E459

�

V462

�K4

63�

E464

�Q4

65�

S466

�GL

UVA

LGL

YSE

RME

TGL

YAL

ALE

ULE

UPH

E

• Molecule 2: Protein transport protein Sec61 subunit gamma

Chain 2:

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


F7�

V8�

E9�

P10

�S1

1R1

2�

Q13

�

L21

C25

T26

K27

P28

D29

�R3

0K3

1�

E32

�F3

3Q3

4K3

5�

I36

�A3

7M3

8�

A39

�T4

0�

A41

�I4

2�

G43

F44

�A4

5�

I46

�M4

7�

G48

�F4

9�

I50

�G5

1F5

2�

F53

�V5

4�

K55

�

H58

�I5

9�

P60

�I6

1�

N62

�N6

3�

I64

�I6

5�

V66

�G6

7�

G68

�

• Molecule 3: Prolactin

Chain w:

R12�

L13�

L14�

L15�

L16�

L17�

V18�

V19

S20�

N21�

L22�

L23�

L24�

C25�

Q26

G27�

V28�

V29�

S30�

• Molecule 4: Protein transport protein Sec61 subunit beta

Chain 3:

X21

�X2

2�

X23

�X2

4�

X25

�X2

6�

X27

�X2

8�

X29

�X3

0X3

1�

X34

�X3

5�

X36

X37

�X3

8�

X39

X40

�X4

1�

X42

�X4

3�

X44

�X4

5�

X46

�X4

7X4

8�

X49

�X5

0�

X51

�X5

2�


4 Experimental information i○

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C1 DepositorNumber of particles used 101339 DepositorResolution determination method Not providedCTF correction method Not providedMicroscope FEI TITAN KRIOS DepositorVoltage (kV) 300 DepositorElectron dose (e−/Å2) 27 DepositorMinimum defocus (nm) 2000 DepositorMaximum defocus (nm) 3500 DepositorMagnification 104478 DepositorImage detector FEI FALCON II (4k x 4k) DepositorMaximum map value 0.667 DepositorMinimum map value -0.407 DepositorAverage map value 0.001 DepositorMap value standard deviation 0.019 DepositorRecommended contour level 0.07 DepositorMap size (Å) 562.8, 562.8, 562.8 wwPDBMap dimensions 420, 420, 420 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.3399999, 1.3399999, 1.3399999 Depositor

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


5 Model quality i○

5.1 Standard geometry i○

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| >51 1 0.58 1/3179 (0.0%) 0.81 7/4305 (0.2%)2 2 0.55 0/504 0.70 0/6733 w 0.51 0/141 0.55 0/191All All 0.58 1/3824 (0.0%) 0.79 7/5169 (0.1%)

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 outliers1 1 0 2

All (1) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)1 1 267 ILE C-N 14.16 1.66 1.34

All (7) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 1 267 ILE O-C-N -18.12 93.71 122.701 1 282 LYS O-C-N 12.99 143.48 122.701 1 282 LYS CA-C-N -10.13 94.92 117.201 1 405 ARG NE-CZ-NH2 7.34 123.97 120.301 1 282 LYS C-N-CA -6.78 104.76 121.701 1 205 ARG CA-CB-CG 5.32 125.10 113.401 1 267 ILE CA-C-N 5.30 128.86 117.20

There are no chirality outliers.

All (2) planarity outliers are listed below:

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


Mol Chain Res Type Group1 1 176 GLY Peptide1 1 198 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 1 3115 0 3246 125 02 2 494 0 527 27 03 w 142 0 168 0 04 3 160 0 34 0 0All All 3911 0 3975 128 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 17.

All (128) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)Clash

overlap (Å)1:1:74:GLY:N 1:1:78:GLU:OE2 1.75 1.18

1:1:187:ILE:CG2 2:2:47:MET:HG3 1.76 1.161:1:267:ILE:CD1 1:1:279:TYR:HB2 1.79 1.131:1:267:ILE:HD12 1:1:279:TYR:HB2 1.18 1.101:1:268:LYS:HD2 1:1:269:SER:O 1.53 1.051:1:199:THR:OG1 1:1:205:ARG:HB3 1.62 0.971:1:187:ILE:HG23 2:2:47:MET:HG3 1.48 0.951:1:187:ILE:HD13 2:2:44:PHE:N 1.85 0.921:1:187:ILE:CG2 2:2:47:MET:CG 2.50 0.901:1:49:PRO:HA 1:1:74:GLY:O 1.75 0.871:1:268:LYS:HB3 1:1:268:LYS:NZ 1.94 0.831:1:187:ILE:HG23 2:2:47:MET:CG 2.09 0.821:1:268:LYS:CD 1:1:269:SER:O 2.26 0.821:1:205:ARG:HG2 1:1:240:PRO:HB3 1.62 0.821:1:187:ILE:CD1 2:2:44:PHE:N 2.41 0.821:1:74:GLY:CA 1:1:78:GLU:OE2 2.30 0.801:1:187:ILE:CD1 2:2:44:PHE:H 1.99 0.751:1:90:ILE:O 1:1:94:LEU:HG 1.87 0.75

Continued on next page...

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


Continued from previous page...


overlap (Å)1:1:244:ASN:OD1 1:1:245:LEU:N 2.22 0.721:1:268:LYS:C 1:1:268:LYS:HD2 2.11 0.71

1:1:267:ILE:CD1 1:1:279:TYR:CB 2.63 0.711:1:256:ILE:HG22 1:1:451:VAL:HG11 1.74 0.681:1:216:LEU:HD12 1:1:242:LEU:HD12 1.76 0.681:1:241:ASN:HB2 1:1:244:ASN:HD21 1.60 0.671:1:267:ILE:HD11 1:1:279:TYR:HB2 1.74 0.671:1:268:LYS:HB3 1:1:268:LYS:HZ3 1.60 0.661:1:230:LEU:HD21 1:1:243:MET:SD 2.36 0.651:1:187:ILE:HG21 2:2:47:MET:CG 2.26 0.651:1:199:THR:CB 1:1:205:ARG:HB3 2.27 0.651:1:187:ILE:HG21 2:2:47:MET:HG3 1.77 0.651:1:401:MET:HB3 1:1:404:HIS:HD2 1.60 0.651:1:262:ARG:NH1 2:2:26:THR:HG21 2.15 0.621:1:400:VAL:HG12 1:1:401:MET:N 2.15 0.621:1:81:ILE:HD13 1:1:178:GLY:HA2 1.81 0.601:1:267:ILE:HD11 1:1:279:TYR:CB 2.31 0.591:1:200:THR:HA 1:1:214:ILE:HB 1.84 0.591:1:205:ARG:HE 1:1:240:PRO:HG2 1.68 0.581:1:434:LEU:O 1:1:438:LEU:HB2 2.04 0.58

1:1:235:TYR:CE1 1:1:239:LEU:HD22 2.40 0.571:1:205:ARG:HA 1:1:240:PRO:HA 1.87 0.571:1:401:MET:CB 1:1:404:HIS:HD2 2.17 0.571:1:268:LYS:HB3 1:1:268:LYS:HZ2 1.69 0.571:1:199:THR:HG1 1:1:205:ARG:HB3 1.67 0.561:1:187:ILE:HD11 2:2:44:PHE:CA 2.35 0.561:1:205:ARG:HE 1:1:240:PRO:CG 2.19 0.551:1:264:ASP:O 1:1:265:LEU:HD23 2.06 0.55

1:1:239:LEU:HD12 1:1:240:PRO:HD2 1.89 0.551:1:264:ASP:C 1:1:265:LEU:HD23 2.26 0.55

1:1:77:MET:HE1 1:1:162:VAL:HG21 1.89 0.551:1:77:MET:CE 1:1:162:VAL:HG21 2.38 0.551:1:205:ARG:HA 1:1:240:PRO:CA 2.36 0.551:1:187:ILE:HD11 2:2:44:PHE:N 2.20 0.551:1:400:VAL:HG12 1:1:401:MET:O 2.08 0.531:1:215:ALA:HB3 1:1:218:HIS:CD2 2.44 0.531:1:262:ARG:CZ 2:2:26:THR:HG21 2.38 0.531:1:187:ILE:CD1 2:2:44:PHE:CA 2.87 0.52

1:1:199:THR:HG23 1:1:214:ILE:C 2.30 0.521:1:199:THR:CB 1:1:205:ARG:CB 2.88 0.521:1:284:PHE:CE1 1:1:428:ILE:HD11 2.45 0.52





overlap (Å)1:1:292:ILE:HD11 1:1:428:ILE:HG21 1.92 0.511:1:205:ARG:HA 1:1:240:PRO:CB 2.41 0.51

1:1:199:THR:HG23 1:1:214:ILE:HG22 1.91 0.511:1:241:ASN:HB2 1:1:244:ASN:ND2 2.26 0.511:1:256:ILE:HB 2:2:36:ILE:HD12 1.92 0.511:1:400:VAL:CG1 1:1:401:MET:N 2.73 0.511:1:242:LEU:O 1:1:245:LEU:HB3 2.11 0.51

1:1:93:LEU:HD21 1:1:379:TRP:CZ3 2.46 0.501:1:74:GLY:C 1:1:78:GLU:OE2 2.50 0.50

1:1:187:ILE:HD11 2:2:44:PHE:H 1.72 0.501:1:86:THR:O 1:1:90:ILE:HG12 2.12 0.49

1:1:256:ILE:HD11 2:2:33:PHE:CE2 2.47 0.491:1:252:PHE:CD2 1:1:447:ILE:HG23 2.48 0.492:2:30:ARG:O 2:2:34:GLN:N 2.44 0.49

1:1:199:THR:OG1 1:1:205:ARG:CB 2.49 0.481:1:206:GLY:N 1:1:240:PRO:HG3 2.28 0.48

1:1:199:THR:HG22 1:1:215:ALA:HA 1.96 0.481:1:193:TRP:HD1 1:1:441:ILE:HG23 1.77 0.481:1:372:CYS:SG 1:1:373:ALA:N 2.87 0.481:1:81:ILE:HG21 1:1:178:GLY:HA2 1.96 0.471:1:199:THR:HB 1:1:205:ARG:HB2 1.96 0.471:1:399:MET:O 1:1:400:VAL:CG2 2.62 0.471:1:261:PHE:CZ 2:2:27:LYS:HG2 2.50 0.472:2:30:ARG:HA 2:2:33:PHE:CB 2.45 0.471:1:81:ILE:HG22 1:1:85:VAL:HG23 1.97 0.461:1:187:ILE:CG2 2:2:47:MET:HG2 2.42 0.461:1:244:ASN:O 1:1:247:ALA:HB3 2.15 0.46

1:1:169:LEU:HD12 1:1:177:SER:HB3 1.98 0.461:1:259:GLN:NE2 1:1:452:THR:HG23 2.31 0.461:1:199:THR:HB 1:1:205:ARG:CB 2.46 0.451:1:196:PHE:CD2 1:1:198:PRO:CD 3.00 0.451:1:399:MET:C 1:1:400:VAL:HG23 2.37 0.45

1:1:413:LEU:HD12 1:1:414:ASN:N 2.31 0.441:1:205:ARG:CG 1:1:240:PRO:HB3 2.39 0.441:1:263:VAL:HG23 2:2:25:CYS:SG 2.58 0.441:1:259:GLN:HE21 1:1:448:LEU:HD12 1.83 0.431:1:244:ASN:ND2 1:1:441:ILE:HG13 2.33 0.431:1:403:GLY:O 1:1:404:HIS:CG 2.71 0.43

1:1:79:LEU:HD22 1:1:127:GLN:HG3 2.01 0.431:1:291:ILE:CG2 1:1:372:CYS:HB2 2.49 0.431:1:26:ILE:HG23 1:1:30:GLU:OE1 2.18 0.43





overlap (Å)1:1:147:ILE:HG22 1:1:151:ILE:HD12 2.01 0.431:1:187:ILE:HG21 2:2:47:MET:HG2 2.00 0.431:1:175:LEU:HD13 1:1:456:GLN:NE2 2.34 0.431:1:399:MET:O 1:1:400:VAL:HG23 2.19 0.431:1:166:ASP:HA 1:1:177:SER:CB 2.49 0.421:1:175:LEU:HG 1:1:176:GLY:N 2.34 0.42

1:1:190:THR:HG22 1:1:194:LYS:HD2 2.00 0.421:1:417:ILE:HB 1:1:418:PRO:CD 2.50 0.421:1:409:MET:O 1:1:410:VAL:C 2.56 0.421:1:387:ALA:HB2 1:1:414:ASN:HD22 1.84 0.411:1:414:ASN:O 1:1:418:PRO:HD2 2.20 0.411:1:183:ILE:CG2 2:2:47:MET:HE3 2.51 0.411:1:205:ARG:NH1 1:1:219:LEU:HB3 2.35 0.411:1:175:LEU:HD13 1:1:456:GLN:CD 2.41 0.411:1:187:ILE:CD1 2:2:44:PHE:HA 2.51 0.411:1:267:ILE:O 1:1:277:ASN:O 2.39 0.411:1:271:ARG:O 1:1:272:TYR:CG 2.74 0.412:2:30:ARG:HA 2:2:33:PHE:HB2 2.02 0.41

1:1:35:THR:HG21 1:1:173:TYR:CE2 2.56 0.411:1:351:PHE:CG 1:1:352:GLY:N 2.88 0.411:1:268:LYS:HD2 1:1:269:SER:N 2.35 0.411:1:267:ILE:HD12 1:1:279:TYR:CB 2.13 0.411:1:74:GLY:N 1:1:78:GLU:CD 2.66 0.411:1:38:THR:HA 1:1:41:ILE:HG22 2.03 0.40

1:1:199:THR:CG2 1:1:215:ALA:CA 3.00 0.401:1:179:ILE:HG23 1:1:453:ILE:HG12 2.04 0.401:1:187:ILE:HD11 2:2:44:PHE:HB2 2.04 0.401:1:282:LYS:O 1:1:285:TYR:HB2 2.22 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.

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


Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 1 393/476 (83%) 333 (85%) 47 (12%) 13 (3%) 4 31

2 2 60/62 (97%) 49 (82%) 6 (10%) 5 (8%) 1 10

3 w 17/19 (90%) 15 (88%) 1 (6%) 1 (6%) 1 18

All All 470/557 (84%) 397 (84%) 54 (12%) 19 (4%) 5 26

All (19) Ramachandran outliers are listed below:

Mol Chain Res Type1 1 205 ARG1 1 287 SER1 1 288 ASN2 2 8 VAL1 1 239 LEU2 2 27 LYS2 2 44 PHE2 2 66 VAL1 1 385 SER1 1 177 SER1 1 238 ASN1 1 261 PHE1 1 448 LEU2 2 49 PHE1 1 345 LEU3 w 13 LEU1 1 176 GLY1 1 202 ASN1 1 211 GLY

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 1 339/398 (85%) 315 (93%) 24 (7%) 14 48

2 2 53/53 (100%) 49 (92%) 4 (8%) 13 45

3 w 18/18 (100%) 17 (94%) 1 (6%) 21 56Continued on next page...

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


Continued from previous page...Mol Chain Analysed Rotameric Outliers Percentiles

All All 410/469 (87%) 381 (93%) 29 (7%) 18 48

All (29) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 1 28 PHE1 1 117 LYS1 1 188 CYS1 1 199 THR1 1 205 ARG1 1 207 MET1 1 226 LYS1 1 239 LEU1 1 240 PRO1 1 252 PHE1 1 268 LYS1 1 271 ARG1 1 275 GLN1 1 290 PRO1 1 294 GLN1 1 346 SER1 1 355 LEU1 1 389 ASP1 1 393 GLN1 1 405 ARG1 1 413 LEU1 1 415 ARG1 1 418 PRO1 1 456 GLN2 2 8 VAL2 2 21 LEU2 2 32 GLU2 2 36 ILE3 w 24 LEU

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (3) suchsidechains are listed below:

Mol Chain Res Type1 1 218 HIS1 1 404 HIS1 1 414 ASN


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○

There are no ligands in this entry.

5.7 Other polymers i○

There are no such residues in this entry.

5.8 Polymer linkage issues i○

The following chains have linkage breaks:

Mol Chain Number of breaks1 1 1

All chain breaks are listed below:

Model Chain Residue-1 Atom-1 Residue-2 Atom-2 Distance (Å)1 1 267:ILE C 268:LYS N 1.66

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_ligandshttps://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 i○

This section contains visualisations of the EMDB entry EMD-3245. 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: 210 Y Index: 210 Z Index: 210

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 i○

6.3.1 Primary map

X Index: 229 Y Index: 212 Z Index: 201

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


7.2 Volume estimate i○

The volume at the recommended contour level is 1648 nm3; this corresponds to an approximatemass of 1489 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 0.278 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-3245 and PDBmodel 3JC2. Per-residue inclusion information can be found in section 3 on page 4.

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 0.07 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 fit 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 i○

At the recommended contour level, 43% of all backbone atoms, 32% 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 i...X50 X51 X52 Page6 FullwwPDBEMValidationReport EMD-3245,3JC2 4...

Documents

Transcript of Full wwPDB EM Validation Report i...X50 X51 X52 Page6 FullwwPDBEMValidationReport EMD-3245,3JC2 4...