Full wwPDB X-ray Structure Validation Report i○

Mar 10, 2018 – 05:41 pm GMT

PDB ID : 4FGCTitle : Crystal Structure of Active Site Mutant C55A of Nitrile Reductase QueF,

Bound to Substrate PreQ0Authors : Stec, B.; Swairjo, M.A.

Deposited on : 2012-06-04Resolution : 2.50 Å(reported)

This is a Full wwPDB X-ray Structure Validation Report for a publicly released PDB entry.

We welcome your comments at validation@mail.wwpdb.orgA user guide is available at

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

MolProbity : 4.02b-467Mogul : 1.7.3 (157068), CSD as539be (2018)

Xtriage (Phenix) : 1.13EDS : trunk30967

Percentile statistics : 20171227.v01 (using entries in the PDB archive December 27th 2017)Refmac : 5.8.0158CCP4 : 7.0 (Gargrove)

Ideal geometry (proteins) : Engh & Huber (2001)Ideal geometry (DNA, RNA) : Parkinson et al. (1996)

Validation Pipeline (wwPDB-VP) : trunk30967

Page 2 Full wwPDB X-ray Structure Validation Report 4FGC

1 Overall quality at a glance i○

The following experimental techniques were used to determine the structure:X-RAY DIFFRACTION

The reported resolution of this entry is 2.50 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)

Similar resolution(#Entries, resolution range(Å))

Rfree 111664 4155 (2.50-2.50)Clashscore 122126 4827 (2.50-2.50)

Ramachandran outliers 120053 4735 (2.50-2.50)Sidechain outliers 120020 4737 (2.50-2.50)RSRZ outliers 108989 4058 (2.50-2.50)

The table below summarises the geometric issues observed across the polymeric chains and their fitto the electron density. The red, orange, yellow and green segments on the lower bar indicate thefraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. Agrey segment 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 theelectron density. The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 A 165

1 B 165

1 C 165

1 D 165

1 E 165

Page 3 Full wwPDB X-ray Structure Validation Report 4FGC

2 Entry composition i○

There are 5 unique types of molecules in this entry. The entry contains 6313 atoms, of which 0are hydrogens and 0 are deuteriums.

In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occu-pancy, the AltConf column contains the number of residues with at least one atom in alternateconformation and the Trace column contains the number of residues modelled with at most 2atoms.

• Molecule 1 is a protein called NADPH-dependent 7-cyano-7-deazaguanine reductase.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 139 Total C N O S1159 754 182 214 9 0 0 0

1 B 145 Total C N O S1212 783 193 227 9 0 0 0

1 C 145 Total C N O S1220 787 194 230 9 0 1 0

1 D 145 Total C N O S1212 783 193 227 9 0 0 0

1 E 145 Total C N O S1221 791 193 228 9 0 1 0

There are 5 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 55 ALA CYS ENGINEERED MUTATION UNP O31678B 55 ALA CYS ENGINEERED MUTATION UNP O31678C 55 ALA CYS ENGINEERED MUTATION UNP O31678D 55 ALA CYS ENGINEERED MUTATION UNP O31678E 55 ALA CYS ENGINEERED MUTATION UNP O31678

• Molecule 2 is 2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE (three-letter code: PQ0) (formula: C7H5N5O).

Page 4 Full wwPDB X-ray Structure Validation Report 4FGC

Mol Chain Residues Atoms ZeroOcc AltConf

2 B 1 Total C N O13 7 5 1 0 0

2 C 1 Total C N O13 7 5 1 0 0

2 D 1 Total C N O13 7 5 1 0 0

2 E 1 Total C N O13 7 5 1 0 0

• Molecule 3 is CALCIUM ION (three-letter code: CA) (formula: Ca).

Mol Chain Residues Atoms ZeroOcc AltConf

3 B 2 Total Ca2 2 0 0

3 D 2 Total Ca2 2 0 0

3 C 2 Total Ca2 2 0 0

3 E 2 Total Ca2 2 0 0

• Molecule 4 is 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL (three-letter code: PE4) (formula: C16H34O8).

Page 5 Full wwPDB X-ray Structure Validation Report 4FGC

Mol Chain Residues Atoms ZeroOcc AltConf

4 B 1 Total C O24 16 8 0 0

• Molecule 5 is water.

Mol Chain Residues Atoms ZeroOcc AltConf

5 A 38 Total O38 38 0 0

5 B 48 Total O48 48 0 0

5 C 36 Total O36 36 0 0

5 D 40 Total O40 40 0 0

5 E 43 Total O43 43 0 0

Page 6 Full wwPDB X-ray Structure Validation Report 4FGC

3 Residue-property plots i○

These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic fora chain summarises the proportions of the various outlier classes displayed in the second graphic.The second graphic shows the sequence view annotated by issues in geometryand electron density.Residues are color-coded according to the number of geometric quality criteria for which theycontain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. A red dotabove a residue indicates a poor fit to the electron density (RSRZ > 2). Stretches of 2 or moreconsecutive residues without any outlier are shown as a green connector. Residues present in thesample, but not in the model, are shown in grey.

• Molecule 1: NADPH-dependent 7-cyano-7-deazaguanine reductase

Chain A:

MET

THR

THR

ARG

LYS

GLU

SER

GLU

LEU

GLU

GLY

VAL

THR

LEU

LEU

GLY

ASN

GLN

GLY

THR

N20•

Y21•

L22

F23

E24

Y25

A26

P27

D28

V29

N35

K36

H37

R40

V44

K45

F46

N47

C48

P49

A55

P56•

K57•

T58•

G59

Q60•

T65

I68

S69

Y70

I71

P72

D73

K83

L84

Y85

L86

F87

S88

F89

R90

N91

F95•

H96•

E97

D98

C99

M100

N101

I102

R114

Y115

I116

E117

V118

W119

G120

K121

F122

R125

G126

S129•

I130

D131

P132

Y133

T134

Y143

N153

H154

D155

L156

Y157•

P158

GLU

THR

ILE

ASP

ASN

ARG

• Molecule 1: NADPH-dependent 7-cyano-7-deazaguanine reductase

Chain B:

MET

THR

THR

ARG

LYS

GLU

SER

GLU

LEU

GLU

GLY

VAL

THR

LEU

LEU

GLY

ASN

GLN

GLY

THR

N20•

Y21•

L22•

F23

E24

Y25

A26

P27

L30

N35

K36

H37

V38

N39•

R40

V44

N47

L54

K57•

T58•

P61

A64

I68

S69

Y70

M76

K80

K83

S88

F89

R90

N91

H92

G93

D94

F95

H96

E97

D98

I102

N105

D106

L110

M111

V118

F122

R125

G126

S129

I130

G140•

M146

R150

H154

D162

N163

R164

• Molecule 1: NADPH-dependent 7-cyano-7-deazaguanine reductase

Chain C:

MET

THR

THR

ARG

LYS

GLU

SER

GLU

LEU

GLU

GLY

VAL

THR

LEU

LEU

GLY

ASN

GLN

GLY

THR

N20•

Y21•

L22

F23•

E24

Y25•

D28

N35

K36

H37

V38

N39

V44

C48

P49

A55

P56

K57•

Q60

P61

A64

T65

Y70

K80

L84

Y85

L86

R90

N91

D94

F95

H96

M100

N101

I102

N105

D106•

V118

K121

F122

G126

S129

I130

D131

P132

Y136

G140•

T141

K142

K145

M152

N153

H154

D155

L156

E159

R164

• Molecule 1: NADPH-dependent 7-cyano-7-deazaguanine reductase

Chain D:

MET

THR

THR

ARG

LYS

GLU

SER

GLU

LEU

GLU

GLY

VAL

THR

LEU

LEU

GLY

ASN

GLN

GLY

THR

N20•

Y21•

L22•

F23

E24

Y25

A26

P27

D28

V29

S32

H37

V38

N39

R40

F43

V44

L54

K57•

T58•

G59

Q60

P61

D62

F63

A64

Y70

I71

P72

M76

K83

L84

Page 7 Full wwPDB X-ray Structure Validation Report 4FGC

Y85

L86

F87

R90

G93

H96

E97

D98

C99

M100

M111

V118

W119

G120

K121

F122

I128

S129

I130

D131

P132

K145

H154

D155

L156

Y157

P158

E159

R164

• Molecule 1: NADPH-dependent 7-cyano-7-deazaguanine reductase

Chain E:

MET

THR

THR

ARG

LYS

GLU

SER

GLU

LEU

GLU

GLY

VAL

THR

LEU

LEU

GLY

ASN

GLN

GLY

THR

N20•

Y21•

L22•

F23

E24

Y25

A26

P27

D28

F33

P34•

N39•

R40

D41

Y42

F43

V44

K45

F46

N47

C48

P49

S53

L54

K57•

T58•

G59•

Q60

P61

T65

Y70

I71

P72

M76

Y85

L86

R90

N91

E97

M100

I103

M111

R114

Y115

I116

E117

V118

G126

G137

K138

K142

Y143

M146

R164

Page 8 Full wwPDB X-ray Structure Validation Report 4FGC

4 Data and refinement statistics i○

Property Value SourceSpace group P 32 2 1 DepositorCell constantsa, b, c, α, β, γ

93.05Å 93.05Å 193.65Å90.00◦ 90.00◦ 120.00◦ Depositor

Resolution (Å) 22.15 – 2.5022.15 – 2.50

DepositorEDS

% Data completeness(in resolution range)

91.5 (22.15-2.50)91.5 (22.15-2.50)

DepositorEDS

Rmerge 0.14 DepositorRsym (Not available) Depositor

< I/σ(I) > 1 2.44 (at 2.50Å) XtriageRefinement program REFMAC 5.5.0109 Depositor

R, Rfree0.228 , 0.3050.233 , 0.298

DepositorDCC

Rfree test set 1592 reflections (5.06%) wwPDB-VPWilson B-factor (Å2) 40.0 Xtriage

Anisotropy 0.202 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.34 , 40.4 EDS

L-test for twinning2 < |L| > = 0.50, < L2 > = 0.33 XtriageEstimated twinning fraction 0.020 for -h,-k,l Xtriage

Fo,Fc correlation 0.91 EDSTotal number of atoms 6313 wwPDB-VP

Average B, all atoms (Å2) 39.0 wwPDB-VP

Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Pattersonfunction is 3.73% of the height of the origin peak. No significant pseudotranslation is detected.

1Intensities estimated from amplitudes.2Theoretical values of < |L| >, < L2 > for acentric reflections are 0.5, 0.333 respectively for untwinned datasets,

and 0.375, 0.2 for perfectly twinned datasets.

Page 9 Full wwPDB X-ray Structure Validation Report 4FGC

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: PQ0,PE4, CA

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 0.73 0/1197 0.89 2/1620 (0.1%)1 B 0.74 0/1250 0.89 0/16911 C 0.74 0/1258 0.85 0/17021 D 0.78 1/1250 (0.1%) 0.92 1/1691 (0.1%)1 E 0.74 0/1263 0.88 0/1709All All 0.74 1/6218 (0.0%) 0.89 3/8413 (0.0%)

All (1) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)1 D 99 CYS CB-SG -5.31 1.73 1.81

All (3) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 A 126 GLY N-CA-C -5.54 99.26 113.101 A 22 LEU CA-CB-CG 5.45 127.83 115.301 D 98 ASP CB-CG-OD1 -5.02 113.78 118.30

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.

Page 10 Full wwPDB X-ray Structure Validation Report 4FGC

Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 A 1159 0 1102 54 01 B 1212 0 1149 47 01 C 1220 0 1153 49 01 D 1212 0 1149 39 01 E 1221 0 1158 46 02 B 13 0 5 3 02 C 13 0 5 1 02 D 13 0 5 0 02 E 13 0 5 0 03 B 2 0 0 0 03 C 2 0 0 0 03 D 2 0 0 0 03 E 2 0 0 0 04 B 24 0 34 0 05 A 38 0 0 8 05 B 48 0 0 4 05 C 36 0 0 5 05 D 40 0 0 5 05 E 43 0 0 4 0All All 6313 0 5765 219 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 18.

All (219) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:B:57:LYS:HG3 1:B:58:THR:H 1.13 1.101:C:23:PHE:CD2 1:C:90:ARG:HD2 2.01 0.961:A:101:ASN:HD21 1:A:134:THR:HG21 1.32 0.941:C:23:PHE:CE2 1:C:90:ARG:HD2 2.07 0.901:A:26:ALA:O 1:A:29:VAL:HG12 1.73 0.881:D:70:TYR:CZ 1:D:111:MET:HE1 2.08 0.871:A:55:ALA:HB1 1:A:56:PRO:HD2 1.58 0.851:A:157:TYR:HB2 5:A:214:HOH:O 1.75 0.851:B:57:LYS:HG3 1:B:58:THR:N 1.94 0.831:C:23:PHE:O 1:C:91:ASN:HB2 1.80 0.821:A:129:SER:O 1:A:130:ILE:HG22 1.78 0.821:B:39:ASN:HB2 5:B:330:HOH:O 1.79 0.815:A:232:HOH:O 1:B:98:ASP:HB3 1.83 0.791:B:57:LYS:CG 1:B:58:THR:H 1.95 0.79

1:A:101:ASN:ND2 1:A:134:THR:HG21 1.98 0.79Continued on next page...

Page 11 Full wwPDB X-ray Structure Validation Report 4FGC

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Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:E:70:TYR:CE2 1:E:111:MET:CE 2.67 0.781:D:76:MET:CE 1:E:97:GLU:HG2 2.14 0.78

1:D:100:MET:HE1 1:D:120:GLY:CA 2.14 0.771:A:129:SER:O 1:A:130:ILE:CG2 2.33 0.77

1:A:153:ASN:HB2 5:A:235:HOH:O 1.84 0.761:D:100:MET:HE1 1:D:120:GLY:HA3 1.68 0.751:E:100:MET:HE3 1:E:118:VAL:CG1 2.16 0.751:A:100:MET:HG3 1:A:132:PRO:HB2 1.67 0.751:B:23:PHE:HB3 1:B:90:ARG:HB3 1.69 0.751:D:70:TYR:CE2 1:D:111:MET:CE 2.70 0.741:B:22:LEU:HD23 1:B:22:LEU:H 1.53 0.741:D:76:MET:HE1 1:E:97:GLU:HG2 1.70 0.731:E:53:SER:O 1:E:54:LEU:HD23 1.88 0.73

1:E:143:TYR:HD2 1:E:146:MET:CE 2.03 0.721:A:40:ARG:NH2 1:B:105:ASN:OD1 2.21 0.721:A:73:ASP:HB3 5:A:216:HOH:O 1.90 0.711:E:70:TYR:CE2 1:E:111:MET:HE3 2.25 0.711:D:70:TYR:CE2 1:D:111:MET:HE2 2.28 0.691:D:87:PHE:HE2 5:D:337:HOH:O 1.77 0.681:C:23:PHE:CD2 1:C:90:ARG:CD 2.77 0.681:E:23:PHE:CD2 1:E:90:ARG:HD2 2.29 0.671:B:22:LEU:HD23 1:B:22:LEU:N 2.09 0.671:E:76:MET:HA 1:E:111:MET:CE 2.25 0.671:C:44:VAL:HG13 1:C:70:TYR:CE1 2.31 0.661:E:46:PHE:HE1 1:E:48:CYS:HB2 1.60 0.661:D:76:MET:HA 1:D:111:MET:HE3 1.78 0.661:A:130:ILE:HD12 1:E:42:TYR:CZ 2.31 0.651:C:142:LYS:HA 1:C:145:LYS:HE3 1.78 0.651:E:100:MET:HE3 1:E:118:VAL:HG12 1.79 0.651:C:24:GLU:OE2 1:C:24:GLU:N 2.30 0.651:C:22:LEU:HD12 1:C:22:LEU:N 2.11 0.651:B:35:ASN:ND2 1:B:37:HIS:H 1.96 0.641:D:70:TYR:CE2 1:D:111:MET:HE1 2.30 0.641:B:146:MET:HG3 1:C:152:MET:HG3 1.80 0.631:A:55:ALA:HB1 1:A:56:PRO:CD 2.26 0.631:D:86:LEU:HB2 5:D:303:HOH:O 1.97 0.631:D:100:MET:CE 1:D:120:GLY:HA3 2.28 0.631:D:25:TYR:CZ 1:D:27:PRO:HG3 2.32 0.631:B:40:ARG:NH2 1:C:105:ASN:OD1 2.33 0.611:B:95:PHE:HD2 2:B:201:PQ0:C5 2.14 0.611:E:49:PRO:HA 1:E:65:THR:HG23 1.82 0.61

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Page 12 Full wwPDB X-ray Structure Validation Report 4FGC

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Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:E:24:GLU:O 1:E:25:TYR:C 2.39 0.611:B:162:ASP:O 1:B:163:ASN:HB2 2.01 0.611:C:121:LYS:HA 1:C:131:ASP:OD1 2.01 0.601:A:130:ILE:HG23 1:A:130:ILE:O 2.01 0.601:D:64:ALA:HB2 1:D:122:PHE:CD2 2.36 0.601:B:47:ASN:HB2 1:C:129:SER:OG 2.02 0.591:C:44:VAL:HG13 1:C:70:TYR:CD1 2.38 0.591:A:156:LEU:CD1 1:A:156:LEU:N 2.66 0.581:A:25:TYR:CE1 1:A:27:PRO:HD3 2.38 0.581:C:91:ASN:HB3 5:C:331:HOH:O 2.02 0.581:D:76:MET:HE2 1:E:97:GLU:HG2 1.84 0.581:A:35:ASN:ND2 1:A:37:HIS:H 2.00 0.581:E:70:TYR:CE2 1:E:111:MET:HE1 2.37 0.581:E:100:MET:CE 1:E:118:VAL:HG12 2.33 0.571:D:32:SER:HA 1:D:76:MET:O 2.04 0.571:D:23:PHE:HB3 1:D:90:ARG:HB3 1.86 0.571:A:25:TYR:HE2 1:A:102:ILE:HG21 1.70 0.561:E:25:TYR:CZ 1:E:27:PRO:HG3 2.40 0.561:E:76:MET:HA 1:E:111:MET:HE2 1.87 0.561:A:155:ASP:HB2 5:E:341:HOH:O 2.05 0.561:C:23:PHE:HD2 1:C:90:ARG:HD2 1.66 0.561:D:70:TYR:OH 1:D:111:MET:HE1 2.06 0.561:C:154:HIS:CD2 1:C:155:ASP:HB2 2.41 0.561:E:46:PHE:CE1 1:E:48:CYS:HB2 2.41 0.551:C:154:HIS:NE2 1:C:155:ASP:HB2 2.21 0.551:C:35:ASN:ND2 1:C:37:HIS:H 2.04 0.551:C:96:HIS:O 1:C:100:MET:HG2 2.06 0.55

1:C:44:VAL:CG1 1:C:70:TYR:CE1 2.89 0.551:B:54:LEU:HD11 1:B:91:ASN:HD22 1.71 0.551:D:70:TYR:HE2 1:D:72:PRO:HB3 1.72 0.551:B:93:GLY:O 1:B:94:ASP:HB3 2.06 0.54

1:D:100:MET:CE 1:D:120:GLY:CA 2.84 0.541:E:143:TYR:HD2 1:E:146:MET:HE2 1.72 0.541:A:44:VAL:HG13 1:A:70:TYR:CE1 2.42 0.541:D:54:LEU:O 1:D:93:GLY:HA2 2.06 0.541:B:76:MET:HA 1:B:111:MET:HE1 1.90 0.541:A:96:HIS:O 1:A:99:CYS:N 2.41 0.54

1:C:49:PRO:HA 1:C:65:THR:HA 1.91 0.521:B:95:PHE:HD2 2:B:201:PQ0:C6 2.22 0.521:B:22:LEU:CD2 1:B:22:LEU:N 2.72 0.521:D:26:ALA:O 1:D:29:VAL:HG12 2.08 0.52

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Page 13 Full wwPDB X-ray Structure Validation Report 4FGC

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Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:A:24:GLU:O 1:A:25:TYR:C 2.48 0.511:E:33:PHE:HB2 1:E:34:PRO:HD2 1.92 0.511:D:100:MET:HE3 1:D:118:VAL:HG12 1.92 0.511:C:48:CYS:SG 1:D:128:ILE:HD12 2.51 0.511:B:68:ILE:HG12 1:B:118:VAL:HG22 1.92 0.511:D:29:VAL:HG21 1:D:84:LEU:HB3 1.92 0.511:D:62:ASP:HA 5:D:307:HOH:O 2.10 0.511:A:49:PRO:HA 1:A:65:THR:HA 1.92 0.511:E:72:PRO:O 1:E:114:ARG:HD2 2.11 0.51

1:C:94[B]:ASP:OD1 1:C:102:ILE:HD12 2.11 0.501:E:25:TYR:CE1 1:E:27:PRO:CG 2.94 0.501:B:70:TYR:CZ 1:B:111:MET:HE1 2.46 0.501:A:23:PHE:CD2 1:A:90:ARG:HD2 2.45 0.501:E:76:MET:HA 1:E:111:MET:HE3 1.91 0.501:A:119:TRP:HE1 1:A:131:ASP:HB3 1.77 0.501:C:39:ASN:HB2 5:C:307:HOH:O 2.11 0.501:E:100:MET:HE3 1:E:118:VAL:HG11 1.90 0.501:B:70:TYR:CE2 1:B:111:MET:CE 2.95 0.491:D:38:VAL:O 1:D:40:ARG:N 2.42 0.49

1:A:100:MET:CG 1:A:132:PRO:HB2 2.41 0.491:A:25:TYR:CD1 1:A:27:PRO:HD3 2.48 0.491:A:83:LYS:HD3 1:B:126:GLY:HA3 1.95 0.491:E:40:ARG:HD2 1:E:42:TYR:CE2 2.47 0.491:C:22:LEU:HD12 1:C:22:LEU:H 1.76 0.491:E:85:TYR:HE2 1:E:103:ILE:HG23 1.76 0.491:E:33:PHE:HB2 1:E:34:PRO:CD 2.43 0.481:C:21:TYR:O 1:C:23:PHE:CE1 2.66 0.48

1:B:30:LEU:HB3 1:B:110:LEU:HD22 1.96 0.481:C:22:LEU:CD1 1:C:22:LEU:H 2.27 0.481:D:29:VAL:HG21 1:D:84:LEU:CB 2.43 0.481:D:60:GLN:HG2 5:D:331:HOH:O 2.14 0.471:C:22:LEU:CD1 1:C:22:LEU:N 2.75 0.471:C:24:GLU:O 1:C:25:TYR:C 2.52 0.471:A:129:SER:C 1:A:130:ILE:HG22 2.34 0.471:B:25:TYR:CE1 1:B:27:PRO:HD3 2.49 0.471:E:60:GLN:HG3 1:E:61:PRO:HD2 1.96 0.471:A:87:PHE:O 1:A:89:PHE:N 2.47 0.471:B:24:GLU:O 1:B:88:SER:HB2 2.15 0.47

1:C:23:PHE:CE2 1:C:90:ARG:CD 2.90 0.461:B:106:ASP:HA 5:B:319:HOH:O 2.15 0.461:A:25:TYR:HE2 1:A:102:ILE:CG2 2.29 0.46

Continued on next page...

Page 14 Full wwPDB X-ray Structure Validation Report 4FGC

Continued from previous page...

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:B:80:LYS:NZ 5:B:340:HOH:O 2.49 0.461:A:130:ILE:CD1 1:E:42:TYR:CE2 2.99 0.461:B:76:MET:HA 1:B:111:MET:CE 2.46 0.451:C:136:TYR:CD1 1:C:136:TYR:C 2.89 0.451:E:25:TYR:CE1 1:E:27:PRO:HG3 2.51 0.451:A:130:ILE:HD12 1:E:42:TYR:CE2 2.49 0.451:B:20:ASN:N 1:B:20:ASN:HD22 2.14 0.45

1:B:20:ASN:ND2 1:B:20:ASN:O 2.48 0.451:C:23:PHE:C 1:C:24:GLU:OE2 2.55 0.451:E:70:TYR:CZ 1:E:111:MET:HE3 2.51 0.45

1:C:100:MET:HE2 1:C:118:VAL:HG12 1.99 0.451:B:162:ASP:O 1:B:163:ASN:CB 2.64 0.451:C:20:ASN:ND2 1:C:21:TYR:N 2.65 0.451:A:25:TYR:CE2 1:A:102:ILE:HG21 2.52 0.451:D:100:MET:HE3 1:D:118:VAL:CG1 2.47 0.451:D:154:HIS:CD2 1:D:155:ASP:HB2 2.52 0.451:B:95:PHE:CD2 2:B:201:PQ0:C5 2.97 0.441:B:83:LYS:HD3 1:C:126:GLY:HA3 1.99 0.441:C:55:ALA:HB1 2:C:201:PQ0:N11 2.32 0.441:C:159:GLU:HG2 5:C:306:HOH:O 2.17 0.441:E:70:TYR:HB3 1:E:116:ILE:HG13 1.99 0.441:A:44:VAL:HG13 1:A:70:TYR:CD1 2.52 0.441:C:23:PHE:HD2 1:C:90:ARG:HB3 1.82 0.441:A:114:ARG:HB3 1:A:143:TYR:CD1 2.53 0.441:A:157:TYR:CB 5:A:214:HOH:O 2.49 0.441:A:56:PRO:HB2 1:A:95:PHE:CE2 2.53 0.441:C:20:ASN:HD22 1:C:20:ASN:N 2.16 0.441:C:100:MET:CE 1:C:118:VAL:HG12 2.48 0.431:E:54:LEU:CD1 1:E:91:ASN:HA 2.48 0.431:A:24:GLU:OE2 1:A:24:GLU:HA 2.18 0.431:B:70:TYR:CE2 1:B:111:MET:HE2 2.53 0.431:C:86:LEU:HB2 5:C:314:HOH:O 2.17 0.431:D:83:LYS:HD3 1:E:126:GLY:HA3 1.99 0.431:E:86:LEU:HA 1:E:86:LEU:HD23 1.83 0.431:E:114:ARG:NE 5:E:307:HOH:O 2.51 0.431:C:80:LYS:O 1:C:84:LEU:HG 2.18 0.43

1:E:24:GLU:OE2 1:E:24:GLU:HA 2.18 0.431:B:163:ASN:HD22 1:B:163:ASN:N 2.16 0.431:C:64:ALA:HB2 1:C:122:PHE:CD2 2.54 0.435:A:232:HOH:O 1:B:102:ILE:HD11 2.19 0.431:C:20:ASN:CG 1:C:21:TYR:H 2.22 0.42

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Page 15 Full wwPDB X-ray Structure Validation Report 4FGC

Continued from previous page...

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:A:125:ARG:CZ 5:A:222:HOH:O 2.67 0.421:B:54:LEU:HD11 1:B:91:ASN:ND2 2.35 0.421:B:61:PRO:O 1:B:125:ARG:NH2 2.43 0.42

1:A:70:TYR:HE2 1:A:72:PRO:HB3 1.84 0.421:C:38:VAL:HG23 1:C:39:ASN:ND2 2.35 0.421:E:142:LYS:O 1:E:146:MET:N 2.47 0.421:B:96:HIS:HD2 1:B:130:ILE:HD12 1.84 0.421:A:45:LYS:HA 1:A:68:ILE:O 2.19 0.41

1:E:44:VAL:HG11 1:E:70:TYR:CZ 2.55 0.411:A:46:PHE:CE2 1:B:130:ILE:HG12 2.55 0.411:C:60:GLN:HG3 1:C:61:PRO:HD2 2.01 0.411:D:100:MET:HG3 1:D:132:PRO:HB2 2.03 0.411:A:116:ILE:HG12 1:A:117:GLU:N 2.36 0.411:C:130:ILE:O 1:C:132:PRO:HD3 2.19 0.411:A:84:LEU:O 1:A:85:TYR:C 2.59 0.41

1:B:64:ALA:HB2 1:B:122:PHE:CD2 2.56 0.411:A:70:TYR:CE2 1:A:72:PRO:HB3 2.56 0.411:E:143:TYR:CD2 1:E:146:MET:CE 2.93 0.411:A:122:PHE:HB2 1:A:130:ILE:HG23 2.01 0.411:A:97:GLU:HA 1:A:97:GLU:OE1 2.20 0.411:A:120:GLY:O 1:A:132:PRO:HD2 2.21 0.411:B:150:ARG:O 1:B:154:HIS:HB2 2.20 0.411:B:98:ASP:O 1:B:102:ILE:HG13 2.21 0.411:D:37:HIS:HD2 5:E:327:HOH:O 2.04 0.411:A:23:PHE:CB 1:A:91:ASN:HD22 2.33 0.411:D:96:HIS:HB3 1:D:122:PHE:CE1 2.56 0.411:E:137:GLY:O 1:E:138:LYS:C 2.58 0.411:B:26:ALA:HB2 5:B:344:HOH:O 2.20 0.411:D:157:TYR:HD1 5:E:340:HOH:O 2.02 0.411:D:159:GLU:HG2 5:D:308:HOH:O 2.21 0.411:D:39:ASN:HD22 1:D:39:ASN:N 2.18 0.411:A:156:LEU:HD12 1:A:156:LEU:N 2.31 0.415:A:221:HOH:O 1:E:45:LYS:HE3 2.20 0.401:E:53:SER:O 1:E:54:LEU:CD2 2.63 0.401:A:129:SER:O 1:A:130:ILE:HG23 2.19 0.401:C:91:ASN:CB 5:C:331:HOH:O 2.66 0.401:D:96:HIS:HD2 1:D:130:ILE:HD12 1.86 0.401:A:96:HIS:O 1:A:97:GLU:C 2.59 0.40

1:A:47:ASN:HB2 1:B:129:SER:OG 2.22 0.401:C:156:LEU:HA 1:C:156:LEU:HD23 1.91 0.40

There are no symmetry-related clashes.

Page 16 Full wwPDB X-ray Structure Validation Report 4FGC

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 X-ray entries followed by that with respect to entriesof similar resolution.

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 137/165 (83%) 125 (91%) 10 (7%) 2 (2%) 11 20

1 B 143/165 (87%) 134 (94%) 8 (6%) 1 (1%) 24 42

1 C 144/165 (87%) 138 (96%) 6 (4%) 0 100 100

1 D 143/165 (87%) 137 (96%) 5 (4%) 1 (1%) 24 42

1 E 144/165 (87%) 133 (92%) 10 (7%) 1 (1%) 24 42

All All 711/825 (86%) 667 (94%) 39 (6%) 5 (1%) 24 42

All (5) Ramachandran outliers are listed below:

Mol Chain Res Type1 A 25 TYR1 A 130 ILE1 E 25 TYR1 B 94 ASP1 D 39 ASN

5.3.2 Protein sidechains i○

In the following table, the Percentiles column shows the percent sidechain outliers of the chain as apercentile score with respect to all X-ray entries followed by that with respect to entries of similarresolution.

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 127/151 (84%) 126 (99%) 1 (1%) 83 94

1 B 134/151 (89%) 130 (97%) 4 (3%) 44 71

1 C 135/151 (89%) 132 (98%) 3 (2%) 55 80

1 D 134/151 (89%) 131 (98%) 3 (2%) 55 80Continued on next page...

Page 17 Full wwPDB X-ray Structure Validation Report 4FGC

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

1 E 135/151 (89%) 133 (98%) 2 (2%) 67 87

All All 665/755 (88%) 652 (98%) 13 (2%) 58 82

All (13) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 35 ASN1 B 20 ASN1 B 22 LEU1 B 44 VAL1 B 91 ASN1 C 20 ASN1 C 28 ASP1 C 35 ASN1 D 43 PHE1 D 44 VAL1 D 145 LYS1 E 28 ASP1 E 44 VAL

Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (13) suchsidechains are listed below:

Mol Chain Res Type1 A 35 ASN1 A 91 ASN1 A 101 ASN1 B 35 ASN1 B 91 ASN1 B 163 ASN1 C 20 ASN1 C 35 ASN1 C 39 ASN1 D 37 HIS1 D 39 ASN1 D 154 HIS1 E 20 ASN

5.3.3 RNA i○

There are no RNA molecules in this entry.

Page 18 Full wwPDB X-ray Structure Validation Report 4FGC

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 carbohydrates in this entry.

5.6 Ligand geometry i○

Of 13 ligands modelled in this entry, 8 are monoatomic - leaving 5 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

2 PQ0 B 201 - 12,14,14 2.29 4 (33%) 11,20,20 3.71 7 (63%)4 PE4 B 203 - 23,23,23 0.65 0 22,22,22 0.54 02 PQ0 C 201 - 12,14,14 2.25 2 (16%) 11,20,20 4.04 7 (63%)2 PQ0 D 201 - 12,14,14 2.26 3 (25%) 11,20,20 3.89 8 (72%)2 PQ0 E 201 - 12,14,14 2.31 3 (25%) 11,20,20 3.76 7 (63%)

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 Rings2 PQ0 B 201 - - 0/0/2/2 0/2/2/24 PE4 B 203 - - 0/21/21/21 0/0/0/02 PQ0 C 201 - - 0/0/2/2 0/2/2/22 PQ0 D 201 - - 0/0/2/2 0/2/2/22 PQ0 E 201 - - 0/0/2/2 0/2/2/2

All (12) bond length outliers are listed below:

Page 19 Full wwPDB X-ray Structure Validation Report 4FGC

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)2 D 201 PQ0 C7-C10 -5.13 1.33 1.442 C 201 PQ0 C7-C10 -5.03 1.33 1.442 E 201 PQ0 C7-C10 -5.01 1.33 1.442 B 201 PQ0 C7-C10 -4.78 1.34 1.442 E 201 PQ0 C7-C5 -2.69 1.38 1.422 B 201 PQ0 C7-C5 -2.57 1.38 1.422 B 201 PQ0 C5-C4 -2.13 1.37 1.432 D 201 PQ0 C6-N1 2.18 1.37 1.332 D 201 PQ0 O6-C6 4.72 1.36 1.242 E 201 PQ0 O6-C6 4.74 1.36 1.242 B 201 PQ0 O6-C6 4.95 1.37 1.242 C 201 PQ0 O6-C6 5.16 1.37 1.24

All (29) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 C 201 PQ0 C8-C7-C10 -7.28 116.72 126.612 C 201 PQ0 C5-C6-N1 -7.07 117.58 124.072 D 201 PQ0 C5-C6-N1 -6.83 117.80 124.072 E 201 PQ0 C5-C6-N1 -6.25 118.33 124.072 D 201 PQ0 C8-C7-C10 -6.01 118.44 126.612 B 201 PQ0 C5-C6-N1 -5.93 118.63 124.072 D 201 PQ0 N3-C2-N1 -4.78 120.40 127.412 C 201 PQ0 N3-C2-N1 -3.63 122.08 127.412 B 201 PQ0 N3-C2-N1 -3.63 122.09 127.412 C 201 PQ0 C7-C5-C4 -3.46 100.48 106.552 E 201 PQ0 N3-C2-N1 -3.45 122.34 127.412 B 201 PQ0 C7-C8-N9 -2.71 103.68 108.912 E 201 PQ0 C7-C8-N9 -2.57 103.95 108.912 D 201 PQ0 C7-C5-C4 -2.52 102.13 106.552 B 201 PQ0 C7-C5-C4 -2.38 102.38 106.552 C 201 PQ0 C7-C8-N9 -2.32 104.42 108.912 D 201 PQ0 C7-C8-N9 -2.22 104.61 108.912 E 201 PQ0 C7-C5-C4 -2.10 102.87 106.552 D 201 PQ0 C2-N3-C4 2.28 117.82 115.162 E 201 PQ0 C2-N3-C4 2.55 118.14 115.162 B 201 PQ0 C2-N3-C4 2.64 118.25 115.162 B 201 PQ0 C6-N1-C2 3.14 120.57 116.062 E 201 PQ0 C6-N1-C2 3.29 120.79 116.062 C 201 PQ0 C6-N1-C2 4.04 121.88 116.062 D 201 PQ0 C6-C5-C4 4.15 117.36 115.022 D 201 PQ0 C6-N1-C2 4.75 122.89 116.062 C 201 PQ0 C6-C5-C4 4.89 117.77 115.02

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Page 20 Full wwPDB X-ray Structure Validation Report 4FGC

Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 B 201 PQ0 C6-C5-C4 8.12 119.59 115.022 E 201 PQ0 C6-C5-C4 8.64 119.88 115.02

There are no chirality outliers.

There are no torsion outliers.

There are no ring outliers.

2 monomers are involved in 4 short contacts:

Mol Chain Res Type Clashes Symm-Clashes2 B 201 PQ0 3 02 C 201 PQ0 1 0

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 21 Full wwPDB X-ray Structure Validation Report 4FGC

6 Fit of model and data i○

6.1 Protein, DNA and RNA chains i○

In the following table, the column labelled ‘#RSRZ> 2’ contains the number (and percentage)of RSRZ outliers, followed by percent RSRZ outliers for the chain as percentile scores relative toall X-ray entries and entries of similar resolution. The OWAB column contains the minimum,median, 95th percentile and maximum values of the occupancy-weighted average B-factor perresidue. The column labelled ‘Q< 0.9’ lists the number of (and percentage) of residues with anaverage occupancy less than 0.9.

Mol Chain Analysed <RSRZ> #RSRZ>2 OWAB(Å2) Q<0.9

1 A 139/165 (84%) 0.19 10 (7%) 15 16 26, 38, 69, 75 0

1 B 145/165 (87%) -0.10 7 (4%) 30 32 22, 34, 48, 75 0

1 C 145/165 (87%) -0.09 7 (4%) 30 32 25, 36, 56, 81 0

1 D 145/165 (87%) -0.29 5 (3%) 45 48 24, 35, 48, 74 0

1 E 145/165 (87%) 0.03 8 (5%) 25 27 27, 39, 58, 87 0

All All 719/825 (87%) -0.05 37 (5%) 28 30 22, 37, 62, 87 0

All (37) RSRZ outliers are listed below:

Mol Chain Res Type RSRZ1 C 25 TYR 9.61 A 95 PHE 6.31 B 20 ASN 5.71 B 21 TYR 5.61 A 56 PRO 5.21 B 57 LYS 4.81 A 57 LYS 4.71 C 20 ASN 4.61 D 21 TYR 4.31 C 57 LYS 4.21 A 20 ASN 4.21 E 58 THR 3.91 E 21 TYR 3.81 B 22 LEU 3.61 C 21 TYR 3.51 A 21 TYR 3.41 D 57 LYS 3.41 E 20 ASN 3.31 E 57 LYS 3.21 D 20 ASN 3.0

Continued on next page...

Page 22 Full wwPDB X-ray Structure Validation Report 4FGC

Continued from previous page...Mol Chain Res Type RSRZ1 C 140 GLY 2.81 E 22 LEU 2.71 B 58 THR 2.71 D 22 LEU 2.61 A 60 GLN 2.51 D 58 THR 2.41 E 59 GLY 2.41 E 34 PRO 2.31 B 39 ASN 2.31 A 58 THR 2.31 E 39 ASN 2.31 A 157 TYR 2.21 A 129 SER 2.21 C 106 ASP 2.11 A 96 HIS 2.11 B 140 GLY 2.01 C 23 PHE 2.0

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

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

6.3 Carbohydrates i○

There are no carbohydrates in this entry.

6.4 Ligands i○

In the following table, the Atoms column lists the number of modelled atoms in the group and thenumber defined in the chemical component dictionary. The B-factors column lists the minimum,median, 95th percentile and maximum values of B factors of atoms in the group. The columnlabelled ‘Q< 0.9’ lists the number of atoms with occupancy less than 0.9.

Mol Type Chain Res Atoms RSCC RSR B-factors(Å2) Q<0.94 PE4 B 203 24/24 0.74 0.23 46,61,64,64 03 CA C 203 1/1 0.90 0.07 56,56,56,56 03 CA B 204 1/1 0.93 0.06 50,50,50,50 02 PQ0 D 201 13/13 0.94 0.12 37,40,45,47 02 PQ0 E 201 13/13 0.94 0.13 41,44,47,48 02 PQ0 C 201 13/13 0.95 0.09 36,40,44,44 0

Continued on next page...

Page 23 Full wwPDB X-ray Structure Validation Report 4FGC

Continued from previous page...Mol Type Chain Res Atoms RSCC RSR B-factors(Å2) Q<0.93 CA D 203 1/1 0.96 0.07 55,55,55,55 02 PQ0 B 201 13/13 0.96 0.14 36,37,41,43 03 CA C 202 1/1 0.98 0.03 40,40,40,40 03 CA B 202 1/1 0.98 0.04 30,30,30,30 03 CA D 202 1/1 0.98 0.03 31,31,31,31 03 CA E 202 1/1 0.98 0.05 26,26,26,26 03 CA E 203 1/1 0.99 0.04 41,41,41,41 0

6.5 Other polymers i○

There are no such residues in this entry.