Full wwPDB EM Validation Report i - RCSB...M211 N215 F216 D217 Q222 S226 L227 G228 F234 D245 I246 Molecule2: ABCtransporterATP-bindingprotein ChainC: M1 K2 L3 E4 K9 S12 D18 I19 D20

Page 1

Full wwPDB EM Validation Report i○

Dec 21, 2020 – 04:21 PM EST

PDB ID : 6XJIEMDB ID : EMD-22211

Title : PmtCD ABC exporter at C1 symmetryAuthors : Zeytuni, N.; Strynadka, N.J.C.; Hu, J.; Worrall, L.J.; Chou, H.; Yu, Z.

Deposited on : 2020-06-23Resolution : 4.00 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) : 2.16

Page 2

Page 2 Full wwPDB EM Validation Report EMD-22211, 6XJI

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 4.00 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 266

1 B 266

2 C 290

2 D 290

Page 3

Page 3 Full wwPDB EM Validation Report EMD-22211, 6XJI

2 Entry composition i○

There are 4 unique types of molecules in this entry. The entry contains 8754 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 Phenol-soluble modulin export ABC transporter permeasesubunit PmtD.

Mol Chain Residues Atoms AltConf Trace

1 A 251 Total C N O S2030 1384 307 333 6 0 0

1 B 251 Total C N O S2030 1384 307 333 6 0 0

There are 42 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA -19 MET - initiating methionine UNP A0A641A693A -18 HIS - expression tag UNP A0A641A693A -17 HIS - expression tag UNP A0A641A693A -16 HIS - expression tag UNP A0A641A693A -15 HIS - expression tag UNP A0A641A693A -14 HIS - expression tag UNP A0A641A693A -13 HIS - expression tag UNP A0A641A693A -12 HIS - expression tag UNP A0A641A693A -11 HIS - expression tag UNP A0A641A693A -10 HIS - expression tag UNP A0A641A693A -9 HIS - expression tag UNP A0A641A693A -8 SER - expression tag UNP A0A641A693A -7 SER - expression tag UNP A0A641A693A -6 GLY - expression tag UNP A0A641A693A -5 LEU - expression tag UNP A0A641A693A -4 VAL - expression tag UNP A0A641A693A -3 PRO - expression tag UNP A0A641A693A -2 ARG - expression tag UNP A0A641A693A -1 GLY - expression tag UNP A0A641A693A 0 SER - expression tag UNP A0A641A693A 1 HIS - expression tag UNP A0A641A693B -19 MET - initiating methionine UNP A0A641A693B -18 HIS - expression tag UNP A0A641A693B -17 HIS - expression tag UNP A0A641A693B -16 HIS - expression tag UNP A0A641A693

Continued on next page...

Page 4

Page 4 Full wwPDB EM Validation Report EMD-22211, 6XJI

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

B -15 HIS - expression tag UNP A0A641A693B -14 HIS - expression tag UNP A0A641A693B -13 HIS - expression tag UNP A0A641A693B -12 HIS - expression tag UNP A0A641A693B -11 HIS - expression tag UNP A0A641A693B -10 HIS - expression tag UNP A0A641A693B -9 HIS - expression tag UNP A0A641A693B -8 SER - expression tag UNP A0A641A693B -7 SER - expression tag UNP A0A641A693B -6 GLY - expression tag UNP A0A641A693B -5 LEU - expression tag UNP A0A641A693B -4 VAL - expression tag UNP A0A641A693B -3 PRO - expression tag UNP A0A641A693B -2 ARG - expression tag UNP A0A641A693B -1 GLY - expression tag UNP A0A641A693B 0 SER - expression tag UNP A0A641A693B 1 HIS - expression tag UNP A0A641A693

• Molecule 2 is a protein called ABC transporter ATP-binding protein.

Mol Chain Residues Atoms AltConf Trace

2 C 290 Total C N O S2315 1475 390 438 12 0 0

2 D 290 Total C N O S2315 1475 390 438 12 0 0

• Molecule 3 is PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER (three-lettercode: AGS) (formula: C10H16N5O12P3S) (labeled as "Ligand of Interest" by depositor).

Page 5

Page 5 Full wwPDB EM Validation Report EMD-22211, 6XJI

Mol Chain Residues Atoms AltConf

3 C 1 Total C N O P S31 10 5 12 3 1 0

3 D 1 Total C N O P S31 10 5 12 3 1 0

• Molecule 4 is MAGNESIUM ION (three-letter code: MG) (formula: Mg) (labeled as "Ligandof Interest" by depositor).

Mol Chain Residues Atoms AltConf

4 D 1 Total Mg1 1 0

4 C 1 Total Mg1 1 0

Page 6

Page 6 Full wwPDB EM Validation Report EMD-22211, 6XJI

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: Phenol-soluble modulin export ABC transporter permease subunit PmtD

Chain A:

MET

HIS

HIS

HIS

HIS

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

V-4

�P-

3�

R-2

�G-

1�

S0�

H1�

R2�

I3�

L4�

I14

�F1

5�

L25

�

I31

�

Q34

�

L37

�M3

8�

A39

�N4

0�

S41

M42

�D4

3�

N44

P45

�K4

6�

H47

�I4

8�

I49

�V5

0Y5

1�

S108

�

S126

N127

�G1

28�

K129

�

D138

�

I157

�

Q162

�

I181

K182

P183

F184

�I1

85�

I188

�P1

89�

R190

�

K194

�

D200

�Y2

01�

F204

�

D209

�K2

10M2

11�

N215

�F2

16�

D217

�F2

18�

S219

N220

�W2

21Q2

22

S229

�

F234

K244

�D2

45�

I246

�

• Molecule 1: Phenol-soluble modulin export ABC transporter permease subunit PmtD

Chain B:

MET

HIS

HIS

HIS

HIS

HIS

HIS

HIS

HIS

HIS

HIS

SER

SER

GLY

LEU

V-4

�P-

3�

R-2

�G-

1S0

�H1

�R2

�I3

�L4

�N5

�

D10

�

K16

�

T20

�

L30

�I3

1A3

2�

S35

�I3

6L3

7M3

8�

A39

�N4

0�

S41

�M4

2�

D43

�N4

4�

P45

�K4

6�

H47

I48

�

Y51

A58

�

G66

�L6

7�

K72

�T7

3

I74

�

A112

�

V117

�I1

18L1

19�

Q123

�A1

24�

S125

S126

�N1

27�

G128

�K1

29�

N130

�L1

31A1

32�

D138

�

Q162

�

I181

K182

P183

F184

I185

�T1

86�

F187

I188

�P1

89R1

90�

Y191

�G1

92E1

93�

K194

�V1

95L1

96�

D197

A198

�F1

99D2

00�

L207

�

M211

�

N215

�F2

16�

D217

�

Q222

�

S226

�L2

27G2

28�

F234

D245

�I2

46�

• Molecule 2: ABC transporter ATP-binding protein

Chain C:

M1�

K2 L3�

E4�

K9�

S12

�

D18

�I1

9D2

0�

F21

D22

F23

G24

�D2

5�

S26

�

K34

N35

K39

�

M43

�

F53

D54

�

D58

�I5

9�

D60

�N6

1�

A62

�D6

3�

L68

I69

E70

K73

�

N77

�

L86

�

D96

�

I104

�D1

05�

M109

�

K119

�Y1

20S1

21M1

22

K137

P138

D151

�P1

52D1

53�

G154

�

D157

�

E168

�L1

69D1

70�

M171

R172

�

H178

K179

L180

E181

�D1

82�

I183

E184

�

C187

�D1

88�

R194

�D1

95�

G196

�

V199

Q200

D201

�

E205

�E2

06�

G207

�V2

08�

A209

S210

�D2

11�

I214

�V2

15T2

16V2

17�

D218

�H2

19�

K220

�D2

21�

F222

D223

�R2

24�

T225

E226

�K2

27�

Y228

�L2

29A2

30�

E231

�H2

32�

Page 7

Page 7 Full wwPDB EM Validation Report EMD-22211, 6XJI

F233

�Q2

34�

L235

Q236

�N2

37�

V238

D239

�K2

40�

A241

�D2

42�

G243

H244

�L2

45�

M246

�I2

47N2

48�

A249

�Q2

50�

K251

�N2

52�

Y253

Q254

V255

I256

�L2

57�

K258

�A2

59�

L260

�S2

61�

E262

�L2

63�

D264

�I2

65�

Y266

�P2

67K2

68�

Y269

I270

�E2

71�

K274

�S2

75�

S276

�L2

77R2

78�

N283

I284

N285

�Q2

86�

R287

�G2

88�

D289

�K2

90�

• Molecule 2: ABC transporter ATP-binding protein

Chain D:

M1�

K2�

L3 E4�

H5�

I6 T7�

G11

�S1

2�

N13

�

D20

�F2

1D2

2F2

3�

G24

�D2

5�

K34

N35

K39

G48

�

I51

�K5

2F5

3

K56

�V5

7D5

8�

I59

�D6

0�

N61

�A6

2�

D63

�

L68

I69

E70

H71

P72

K73

N77

�

Y82

�

V90

�L9

1�

G92

K93

�G9

4�

F95

D96

�

Y99

�T1

00

D101

�K1

02�

I103

I104

�D1

05�

K118

�K1

19�

Y120

S121

�M1

22

A129

K137

�P1

38

D144

�

D151

�P1

52D1

53�

D157

�

K163

�S1

64L1

65�

E168

�L1

69�

D170

�

H178

K179

�L1

80E1

81�

D182

�

L185

�I1

86�

C187

�D1

88�

R194

�D1

95G1

96�

Q200

D201

�V2

02N2

03�

M204

�E2

05�

E206

�G2

07V2

08�

A209

�S2

10�

D211

�

T212

T213

I214

V215

�

D218

�H2

19�

K220

�D2

21F2

22�

D223

�R2

24�

T225

�E2

26�

K227

�Y2

28�

L229

�A2

30�

E231

�H2

32�

F233

�Q2

34�

L235

�Q2

36�

N237

�V2

38�

D239

�K2

40�

A241

�D2

42�

G243

�H2

44�

L245

�M2

46�

I247

�N2

48�

A249

�Q2

50�

K251

�N2

52�

Y253

�Q2

54�

V255

�I2

56L2

57�

K258

�A2

59L2

60�

S261

E262

�L2

63�

D264

�I2

65Y2

66�

P267

K268

�Y2

69�

I270

E271

�T2

72

R273

�K2

74�

S275

�S2

76�

L277

�R2

78�

D279

�T2

80�

Y281

�F2

82�

N283

I284

�N2

85�

Q286

�R2

87�

G288

�D2

89�

K290

�

Page 8

Page 8 Full wwPDB EM Validation Report EMD-22211, 6XJI

4 Experimental information i○

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, Not providedNumber of particles used 113197 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

) 1.16 DepositorMinimum defocus (nm) Not providedMaximum defocus (nm) Not providedMagnification Not providedImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 0.259 DepositorMinimum map value -0.179 DepositorAverage map value 0.000 DepositorMap value standard deviation 0.009 DepositorRecommended contour level 0.0552 DepositorMap size (Å) 196.49998, 196.49998, 196.49998 wwPDBMap dimensions 150, 150, 150 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.31, 1.31, 1.31 Depositor

Page 9

Page 9 Full wwPDB EM Validation Report EMD-22211, 6XJI

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: MG,AGS

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 0.99 2/2083 (0.1%) 0.84 1/2828 (0.0%)1 B 0.99 2/2083 (0.1%) 0.84 1/2828 (0.0%)2 C 0.91 2/2351 (0.1%) 0.87 5/3156 (0.2%)2 D 0.88 2/2351 (0.1%) 0.81 1/3156 (0.0%)All All 0.94 8/8868 (0.1%) 0.84 8/11968 (0.1%)

All (8) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)2 C 199 VAL C-N 7.67 1.51 1.341 B 222 GLN CB-CG -5.95 1.36 1.521 A 222 GLN CB-CG -5.94 1.36 1.521 B 234 PHE CB-CG -5.66 1.41 1.511 A 234 PHE CB-CG -5.66 1.41 1.512 D 53 PHE CB-CG -5.55 1.42 1.512 C 53 PHE CB-CG -5.53 1.42 1.512 D 266 TYR C-N -5.49 1.23 1.34

All (8) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 D 120 TYR CB-CG-CD2 -7.21 116.67 121.002 C 120 TYR CB-CG-CD2 -7.17 116.70 121.002 C 270 ILE O-C-N -6.87 111.71 122.702 C 194 ARG NE-CZ-NH1 6.80 123.70 120.302 C 215 VAL O-C-N -6.56 112.21 122.702 C 270 ILE C-N-CA 5.40 135.20 121.701 B 51 TYR CB-CG-CD1 -5.35 117.79 121.001 A 51 TYR CB-CG-CD1 -5.29 117.82 121.00

Page 10

Page 10 Full wwPDB EM Validation Report EMD-22211, 6XJI

There are no chirality outliers.

There are no planarity outliers.

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 2030 0 2158 6 01 B 2030 0 2158 6 02 C 2315 0 2361 37 02 D 2315 0 2361 38 03 C 31 0 12 1 03 D 31 0 12 1 04 C 1 0 0 0 04 D 1 0 0 0 0All All 8754 0 9062 77 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 4.

All (77) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

2:C:241:ALA:CB 2:C:290:LYS:HD3 1.60 1.292:C:241:ALA:HB1 2:C:290:LYS:HD3 1.33 1.072:C:241:ALA:HB2 2:C:290:LYS:HD3 1.34 1.022:C:241:ALA:CB 2:C:290:LYS:CD 2.44 0.952:D:212:THR:CG2 2:D:236:GLN:OE1 2.19 0.902:C:241:ALA:HB2 2:C:290:LYS:CD 2.02 0.882:C:180:LEU:CD1 2:C:278:ARG:HA 2.08 0.842:D:180:LEU:CD1 2:D:278:ARG:HA 2.08 0.842:D:214:ILE:HD12 2:D:271:GLU:OE2 1.76 0.842:C:214:ILE:HD11 2:C:244:HIS:HB3 1.64 0.792:C:214:ILE:CD1 2:C:244:HIS:HB3 2.11 0.79

2:D:212:THR:HG21 2:D:236:GLN:OE1 1.85 0.752:D:212:THR:HG22 2:D:236:GLN:OE1 1.85 0.742:C:254:GLN:HG3 2:D:268:LYS:HG2 1.75 0.69

2:D:39:LYS:N 3:D:301:AGS:O1B 2.26 0.68Continued on next page...

Page 11

Page 11 Full wwPDB EM Validation Report EMD-22211, 6XJI

Continued from previous page...

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

2:C:39:LYS:N 3:C:301:AGS:O1B 2.26 0.672:C:237:ASN:ND2 2:C:283:ASN:ND2 2.44 0.662:C:237:ASN:HD22 2:C:283:ASN:CG 2.00 0.652:C:180:LEU:HD12 2:C:278:ARG:HA 1.80 0.642:D:211:ASP:OD1 2:D:274:LYS:HG3 1.99 0.622:D:180:LEU:HD12 2:D:278:ARG:HA 1.80 0.622:D:214:ILE:HG12 2:D:246:MET:HG2 1.80 0.612:C:122:MET:HB2 2:D:70:GLU:OE1 2.02 0.592:C:70:GLU:OE1 2:D:122:MET:HB2 2.02 0.592:C:34:LYS:HG3 2:D:151:ASP:OD2 2.05 0.572:C:214:ILE:HD11 2:C:244:HIS:CB 2.32 0.572:C:2:LYS:NZ 2:C:22:ASP:OD2 2.37 0.56

2:C:151:ASP:OD2 2:D:34:LYS:HG3 2.05 0.562:C:237:ASN:HD22 2:C:283:ASN:ND2 2.03 0.552:C:180:LEU:HD13 2:C:278:ARG:HA 1.87 0.552:C:237:ASN:ND2 2:C:283:ASN:CG 2.59 0.552:D:236:GLN:NE2 2:D:248:ASN:OD1 2.40 0.552:D:218:ASP:OD1 2:D:268:LYS:HE3 2.06 0.552:D:212:THR:HG21 2:D:246:MET:HE3 1.91 0.532:C:214:ILE:HD13 2:C:244:HIS:HB3 1.91 0.522:D:2:LYS:NZ 2:D:22:ASP:OD2 2.37 0.52

2:D:180:LEU:HD13 2:D:278:ARG:HA 1.87 0.522:D:211:ASP:CG 2:D:274:LYS:HG3 2.30 0.522:C:180:LEU:CD1 2:C:278:ARG:CA 2.86 0.492:D:180:LEU:CD1 2:D:278:ARG:CA 2.86 0.492:C:270:ILE:CG2 2:D:270:ILE:CD1 2.90 0.492:D:218:ASP:OD1 2:D:268:LYS:NZ 2.43 0.492:C:34:LYS:HG2 2:C:35:ASN:N 2.28 0.492:D:34:LYS:HG2 2:D:35:ASN:N 2.28 0.481:A:126:SER:OG 1:A:127:ASN:N 2.47 0.482:C:137:LYS:N 2:C:138:PRO:HD3 2.30 0.47

2:D:214:ILE:HD12 2:D:271:GLU:CD 2.34 0.472:C:254:GLN:CG 2:D:268:LYS:HG2 2.45 0.471:B:126:SER:OG 1:B:127:ASN:N 2.47 0.472:D:137:LYS:N 2:D:138:PRO:HD3 2.30 0.46

2:D:218:ASP:OD1 2:D:268:LYS:CE 2.65 0.452:D:201:ASP:OD1 2:D:202:VAL:N 2.49 0.452:D:200:GLN:OE1 2:D:284:ILE:HD11 2.17 0.452:C:178:HIS:O 2:C:179:LYS:HB2 2.18 0.442:C:214:ILE:O 2:C:270:ILE:HA 2.18 0.44

2:C:180:LEU:HD13 2:C:278:ARG:CA 2.47 0.44Continued on next page...

Page 12

Page 12 Full wwPDB EM Validation Report EMD-22211, 6XJI

Continued from previous page...

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

2:D:178:HIS:O 2:D:179:LYS:HB2 2.18 0.442:C:180:LEU:HD13 2:C:278:ARG:N 2.33 0.431:B:182:LYS:HB2 1:B:183:PRO:HD3 2.01 0.432:D:180:LEU:HD13 2:D:278:ARG:N 2.33 0.431:A:182:LYS:HB2 1:A:183:PRO:HD3 2.01 0.422:C:241:ALA:HB2 2:C:290:LYS:HD2 1.97 0.422:C:270:ILE:CG2 2:D:270:ILE:HD12 2.49 0.422:C:180:LEU:HD13 2:C:277:LEU:C 2.40 0.422:C:137:LYS:N 2:C:138:PRO:CD 2.83 0.421:B:181:ILE:O 1:B:182:LYS:C 2.59 0.41

2:D:180:LEU:HD13 2:D:278:ARG:CA 2.47 0.411:B:188:ILE:N 1:B:189:PRO:HD2 2.36 0.411:A:37:LEU:O 1:B:190:ARG:NH1 2.54 0.412:D:137:LYS:N 2:D:138:PRO:CD 2.83 0.411:A:181:ILE:O 1:A:182:LYS:C 2.59 0.41

2:C:180:LEU:HD12 2:C:278:ARG:CA 2.50 0.412:D:180:LEU:HD13 2:D:277:LEU:C 2.41 0.41

1:A:188:ILE:N 1:A:189:PRO:HD2 2.36 0.402:D:72:PRO:HB3 2:D:129:ALA:HB2 2.03 0.402:D:180:LEU:HD12 2:D:278:ARG:CA 2.50 0.401:A:190:ARG:NH1 1:B:37:LEU:O 2.54 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 249/266 (94%) 246 (99%) 3 (1%) 0 100 100

1 B 249/266 (94%) 246 (99%) 3 (1%) 0 100 100

2 C 288/290 (99%) 283 (98%) 5 (2%) 0 100 100

2 D 288/290 (99%) 283 (98%) 5 (2%) 0 100 100Continued on next page...

Page 13

Page 13 Full wwPDB EM Validation Report EMD-22211, 6XJI

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

All All 1074/1112 (97%) 1058 (98%) 16 (2%) 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 227/241 (94%) 227 (100%) 0 100 100

1 B 227/241 (94%) 227 (100%) 0 100 100

2 C 258/258 (100%) 255 (99%) 3 (1%) 71 84

2 D 258/258 (100%) 252 (98%) 6 (2%) 50 70

All All 970/998 (97%) 961 (99%) 9 (1%) 79 88

All (9) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type2 C 68 LEU2 C 69 ILE2 C 73 LYS2 D 68 LEU2 D 69 ILE2 D 73 LYS2 D 270 ILE2 D 271 GLU2 D 273 ARG

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (2) suchsidechains are listed below:

Mol Chain Res Type2 C 237 ASN2 C 283 ASN

Page 14

Page 14 Full wwPDB EM Validation Report EMD-22211, 6XJI

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○

Of 4 ligands modelled in this entry, 2 are monoatomic - leaving 2 for Mogul analysis.

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 bondlength (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

Mol Type Chain Res Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

3 AGS C 301 4 26,33,33 0.60 0 26,52,52 0.70 1 (3%)3 AGS D 301 4 26,33,33 0.60 0 26,52,52 0.70 1 (3%)

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 Rings3 AGS C 301 4 - 2/17/38/38 0/3/3/33 AGS D 301 4 - 2/17/38/38 0/3/3/3

There are no bond length outliers.

All (2) bond angle outliers are listed below:

Page 15

Page 15 Full wwPDB EM Validation Report EMD-22211, 6XJI

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)3 C 301 AGS C5-C6-N6 2.22 123.72 120.353 D 301 AGS C5-C6-N6 2.20 123.69 120.35

There are no chirality outliers.

All (4) torsion outliers are listed below:

Mol Chain Res Type Atoms3 C 301 AGS PG-O3B-PB-O2B3 D 301 AGS PG-O3B-PB-O2B3 C 301 AGS C5’-O5’-PA-O1A3 D 301 AGS C5’-O5’-PA-O1A

There are no ring outliers.

2 monomers are involved in 2 short contacts:

Mol Chain Res Type Clashes Symm-Clashes3 C 301 AGS 1 03 D 301 AGS 1 0

The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. Inaddition, ligands with molecular weight > 250 and outliers as shown on the validation Tables willalso be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles iswithin 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier.Any bond that is central to one or more torsion angles 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.

Page 16

Page 16 Full wwPDB EM Validation Report EMD-22211, 6XJI

Ligand AGS C 301

Bond lengths Bond angles

Torsions Rings

Page 17

Page 17 Full wwPDB EM Validation Report EMD-22211, 6XJI

Ligand AGS D 301

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.

Page 18

Page 18 Full wwPDB EM Validation Report EMD-22211, 6XJI

6 Map visualisation i○

This section contains visualisations of the EMDB entry EMD-22211. 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: 75 Y Index: 75 Z Index: 75

Page 19

Page 19 Full wwPDB EM Validation Report EMD-22211, 6XJI

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: 79 Y Index: 82 Z Index: 64

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 0.0552.These images, in conjunction with the slice images, may facilitate assessment of whether an ap-propriate contour level has been provided.

Page 20

Page 20 Full wwPDB EM Validation Report EMD-22211, 6XJI

6.5 Mask visualisation i○

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

Page 21

Page 21 Full wwPDB EM Validation Report EMD-22211, 6XJI

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.

Page 22

Page 22 Full wwPDB EM Validation Report EMD-22211, 6XJI

7.2 Volume estimate i○

The volume at the recommended contour level is 39 nm3; this corresponds to an approximate massof 35 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.

Page 23

Page 23 Full wwPDB EM Validation Report EMD-22211, 6XJI

7.3 Rotationally averaged power spectrum i○

*Reported resolution corresponds to spatial frequency of 0.250 Å−1

Page 24

Page 24 Full wwPDB EM Validation Report EMD-22211, 6XJI

8 Fourier-Shell correlation i○

Fourier-Shell Correlation (FSC) is the most commonly used method to estimate the resolution ofsingle-particle and subtomogram-averaged maps. The shape of the curve depends on the imposedsymmetry, mask and whether or not the two 3D reconstructions used were processed from acommon reference. The reported resolution is shown as a black line. A curve is displayed for thehalf-bit criterion in addition to lines showing the 0.143 gold standard cut-off and 0.5 cut-off.

8.1 FSC i○

*Reported resolution corresponds to spatial frequency of 0.250 Å−1

Page 25

Page 25 Full wwPDB EM Validation Report EMD-22211, 6XJI

8.2 Resolution estimates i○

Resolution estimate (Å) Estimation criterion (FSC cut-off)0.143 0.5 Half-bit

Reported by author 4.00 - -Author-provided FSC curve 4.04 4.46 4.10

Calculated* - - -

*Resolution estimate based on FSC curve calculated by comparison of deposited half-maps.

Page 26

Page 26 Full wwPDB EM Validation Report EMD-22211, 6XJI

9 Map-model fit i○

This section contains information regarding the fit between EMDB map EMD-22211 and PDBmodel 6XJI. 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 0.0552at 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.

Page 27

Page 27 Full wwPDB EM Validation Report EMD-22211, 6XJI

9.2 Atom inclusion i○

At the recommended contour level, 65% of all backbone atoms, 49% of all non-hydrogen atoms,are inside the map.