full wwpdb x-ray structure validation report i

Full wwPDB X-ray Structure Validation Report i○

Apr 13, 2021 – 08:01 PM EDT

PDB ID : 3HRWTitle : Crystal structure of hemoglobin from mouse (Mus musculus)at 2.8

Authors : Sundaresan, S.S.; Ramesh, P.; Ponnuswamy, M.N.Deposited on : 2009-06-10

Resolution : 2.80 Å(reported)

This is a Full wwPDB X-ray Structure 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/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 : 1.8.5 (274361), CSD as541be (2020)

Xtriage (Phenix) : 1.13EDS : 2.18

buster-report : 1.1.7 (2018)Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)

Refmac : 5.8.0158CCP4 : 7.0.044 (Gargrove)

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

Validation Pipeline (wwPDB-VP) : 2.18

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



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

Full wwPDB X-ray Structure Validation Report 3HRW

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 2.80 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 130704 3140 (2.80-2.80)Clashscore 141614 3569 (2.80-2.80)

Ramachandran outliers 138981 3498 (2.80-2.80)Sidechain outliers 138945 3500 (2.80-2.80)RSRZ outliers 127900 3078 (2.80-2.80)

The table below summarises the geometric issues observed across the polymeric chains and theirfit to the electron density. The red, orange, yellow and green segments of the lower bar indicatethe fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric qualitycriteria respectively. A grey segment represents the fraction of residues that are not modelled.The numeric value for each fraction is indicated below the corresponding segment, with a dotrepresenting fractions <=5% The upper red bar (where present) indicates the fraction of residuesthat have poor fit to the electron density. The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 A 141

1 C 141

2 B 146

2 D 146

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


2 Entry composition i○

There are 4 unique types of molecules in this entry. The entry contains 4548 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 Hemoglobin subunit alpha.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 141 Total C N O S1057 674 187 194 2 0 0 0

1 C 141 Total C N O S1057 674 187 194 2 0 0 0

• Molecule 2 is a protein called Hemoglobin subunit beta-1.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

2 B 146 Total C N O S1108 708 195 201 4 0 0 0

2 D 146 Total C N O S1108 708 195 201 4 0 0 0

• Molecule 3 is PROTOPORPHYRIN IX CONTAINING FE (three-letter code: HEM) (for-mula: C34H32FeN4O4).

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


Mol Chain Residues Atoms ZeroOcc AltConf

3 A 1 Total C Fe N O43 34 1 4 4 0 0

3 B 1 Total C Fe N O43 34 1 4 4 0 0

3 C 1 Total C Fe N O43 34 1 4 4 0 0

3 D 1 Total C Fe N O43 34 1 4 4 0 0

• Molecule 4 is water.

Mol Chain Residues Atoms ZeroOcc AltConf

4 A 15 Total O15 15 0 0

4 B 9 Total O9 9 0 0

4 C 12 Total O12 12 0 0

4 D 10 Total O10 10 0 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 andelectron density. Residues are color-coded according to the number of geometric quality criteriafor which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more.A red dot above a residue indicates a poor fit to the electron density (RSRZ > 2). Stretches of 2or more consecutive residues without any outlier are shown as a green connector. Residues presentin the sample, but not in the model, are shown in grey.

• Molecule 1: Hemoglobin subunit alpha

Chain A:

V1 G4 E5 D6 K7 S8 N9 I10

K11

A12

G15

K16

I17

G18

G19

H20•

G21

A22

E23

Y24

E27

R31

M32

S35

F36

P37

T38

T39

K40

T41

Y42

H45

F46

D47

V48

H58

G59

K60

A69

A70

G71

H72•

L73

D74

D75

L76

L80

L83

S84

D85

L86

H87

A88

H89

K90

L91

R92

V93

D94

P95

V96

N97

F98

S102

L105

T108

S111

H112

H113

D116

F117

T118

P119

A120

V121

H122

A123

S124

L125

D126

K127

F128

L129

A130

S131

V135

L136

T137

S138

K139

Y140•

R141•

• Molecule 1: Hemoglobin subunit alpha

Chain C:

V1•

L2 S3 G4 E5 D6 K7 S8 N9 I10

K11

A12

A13

W14

I17

G18

G19•

A22

E23

Y24

G25

R31

M32

S35

F36

P37

T38

T39

K40

T41

Y42

H45

F46

D47

V48

S49

H50

G51

S52

A53

Q54

V55

H58

G59

K60

K61

V62

L66

A69

D75•

L76

P77

G78

A79

L80

S81

A82

L83

S84

D85

L86

K90

L91

R92

V93

D94

N97

F98

K99

L100

L101

S102

H103

C104

L105

L106

V107

S111

H112

H113

P114

F117

T118

P119

A123

S124

L125

D126

K127

V135

L136

T137

S138•

K139

Y140

R141•

• Molecule 2: Hemoglobin subunit beta-1

Chain B:

V1 H2•

L3 T4 E7 K8 V11

L14

W15

V18

N19

S20

D21

E22

V23

G24

G25

E26

A27

L28

G29

R30

L31

L32

V33

V34

Y35

P36

W37

T38

Q39

R40

Y41

F42

D43

S44

F45

G46

D47

M55

H63

G64

K65

K66

V67

I68

T69

A70

F71

N72

D73

G74

L75

N76

H77

L78

D79

S80

L81

K82

S87

L88

S89

E90

L91

H92

C93•

D94

K95

L96

H97

V98

D99

P100

F103

R104

L105

L106

M109

I110

V111

I112

V113

L114

G115

L118

G119

F122

T123

P124

A125

A126

Q127

A128

A129

F130

Q131

K132

V133

V137

L141

A142

H143

K144

Y145•

H146•

• Molecule 2: Hemoglobin subunit beta-1

Chain D:

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


V1 H2•

L3 T4•

D5•

A6•

E7 K8 A9 A10

V11

S12

C13

L14

N19

S20

D21

E22

V23

G24

G25

E26

A27

L28

G29

R30

L31

L32

V33

V34

Y35

P36

W37

T38

Q39

R40

Y41

F42

D43

S44

F45

L48

S49

S50

A53

I54

N57

A58

K59

V60

H63

V67

I68

N72

D73

G74

L75

N76

H77

S80

L81

K82

F85

A86

S87

L88

S89

H92

C93

D94

K95

V98

D99

P100

E101

N102

F103

R104

L105

L106

G107

V113

L118

G119

K120

D121

F122

T123

P124

A125

A126

Q127

A128

A129

F130

V134

A140

L141

A142

H143

K144

Y145

H146•


4 Data and refinement statistics i○

Property Value SourceSpace group P 21 21 21 DepositorCell constantsa, b, c, α, β, γ

53.08Å 65.94Å 150.93Å90.00◦ 90.00◦ 90.00◦ Depositor

Resolution (Å) 19.94 – 2.8019.94 – 2.80

DepositorEDS

% Data completeness(in resolution range)

92.9 (19.94-2.80)92.9 (19.94-2.80)

DepositorEDS

Rmerge (Not available) DepositorRsym 0.11 Depositor

< I/σ(I) > 1 1.59 (at 2.79Å) XtriageRefinement program REFMAC 5.2.0019 Depositor

R, Rfree0.243 , 0.3060.240 , 0.299

DepositorDCC

Rfree test set 616 reflections (4.88%) wwPDB-VPWilson B-factor (Å2) 47.1 Xtriage

Anisotropy 0.236 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.28 , 51.9 EDS

L-test for twinning2 < |L| > = 0.46, < L2 > = 0.29 XtriageEstimated twinning fraction No twinning to report. Xtriage

Fo,Fc correlation 0.90 EDSTotal number of atoms 4548 wwPDB-VP

Average B, all atoms (Å2) 36.0 wwPDB-VP

Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Pattersonfunction is 5.29% 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.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#data_stats


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:HEM

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 0.49 0/1085 0.76 5/1471 (0.3%)1 C 0.49 0/1085 0.70 0/14712 B 0.53 0/1133 0.85 4/1534 (0.3%)2 D 0.50 0/1133 0.79 3/1534 (0.2%)All All 0.50 0/4436 0.78 12/6010 (0.2%)

There are no bond length outliers.

All (12) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 B 88 LEU CB-CA-C -9.06 92.98 110.202 D 81 LEU CB-CA-C -8.01 94.99 110.202 D 81 LEU N-CA-C 6.17 127.65 111.002 D 19 ASN CB-CA-C 5.76 121.92 110.401 A 88 ALA CB-CA-C -5.62 101.66 110.102 B 96 LEU CB-CA-C -5.62 99.52 110.201 A 36 PHE N-CA-C -5.61 95.86 111.001 A 89 HIS CB-CA-C -5.35 99.70 110.401 A 105 LEU CA-CB-CG 5.28 127.45 115.302 B 35 TYR N-CA-C -5.24 96.85 111.002 B 2 HIS CB-CA-C 5.19 120.78 110.401 A 75 ASP N-CA-C -5.14 97.11 111.00

There are no chirality outliers.

There are no planarity outliers.

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

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


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 1057 0 1048 83 01 C 1057 0 1048 83 02 B 1108 0 1105 95 02 D 1108 0 1105 83 03 A 43 0 30 8 03 B 43 0 30 7 03 C 43 0 30 9 03 D 43 0 30 7 04 A 15 0 0 0 04 B 9 0 0 2 04 C 12 0 0 1 04 D 10 0 0 2 0All All 4548 0 4426 318 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 36.

All (318) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

2:B:36:PRO:O 2:B:39:GLN:HG2 1.48 1.121:A:83:LEU:HD13 3:A:200:HEM:HHB 1.36 1.082:B:32:LEU:H 2:B:32:LEU:HD23 1.10 1.062:B:87:SER:O 2:B:88:LEU:HB2 1.44 1.061:C:3:SER:HB2 1:C:4:GLY:HA2 1.36 1.041:C:3:SER:CB 1:C:4:GLY:HA2 1.89 1.022:B:20:SER:O 2:B:68:ILE:HD12 1.60 1.012:B:35:TYR:O 2:B:38:THR:HG22 1.61 1.001:A:6:ASP:OD2 1:A:127:LYS:HE2 1.60 0.992:D:63:HIS:HE1 4:D:147:HOH:O 1.47 0.962:B:32:LEU:H 2:B:32:LEU:CD2 1.78 0.951:C:32:MET:SD 1:C:39:THR:HG21 2.07 0.941:A:95:PRO:HG3 1:A:140:TYR:OH 1.69 0.921:A:141:ARG:CZ 1:C:1:VAL:HG21 2.01 0.912:B:68:ILE:HA 2:B:71:PHE:HB3 1.52 0.89

Continued on next page...

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


Continued from previous page...


Clashoverlap (Å)

1:C:24:TYR:HE1 1:C:112:HIS:HD1 1.22 0.872:D:100:PRO:HD3 2:D:145:TYR:CE1 2.09 0.862:D:63:HIS:CE1 4:D:147:HOH:O 2.22 0.861:A:16:LYS:HD2 1:A:116:ASP:OD2 1.77 0.841:A:83:LEU:CD1 3:A:200:HEM:HHB 2.09 0.832:B:32:LEU:HD23 2:B:32:LEU:N 1.94 0.822:D:34:VAL:HG23 2:D:35:TYR:CD2 2.17 0.801:C:24:TYR:HE1 1:C:112:HIS:ND1 1.81 0.792:B:72:ASN:HA 2:B:75:LEU:HD12 1.62 0.79

1:A:83:LEU:HD13 3:A:200:HEM:CHB 2.11 0.781:A:119:PRO:HG3 2:B:55:MET:HE3 1.65 0.782:B:137:VAL:O 2:B:141:LEU:HD23 1.83 0.782:D:24:GLY:N 2:D:68:ILE:HD11 2.00 0.772:D:22:GLU:O 2:D:26:GLU:HB2 1.85 0.771:C:103:HIS:O 1:C:107:VAL:HG23 1.85 0.762:B:19:ASN:O 2:B:20:SER:CB 2.32 0.76

3:D:200:HEM:HHC 3:D:200:HEM:HBB2 1.69 0.742:B:68:ILE:HA 2:B:71:PHE:CB 2.17 0.742:B:68:ILE:O 2:B:71:PHE:N 2.21 0.73

1:C:58:HIS:HE1 3:C:200:HEM:C1A 2.06 0.731:C:99:LYS:HB2 1:C:99:LYS:NZ 2.04 0.732:B:19:ASN:O 2:B:20:SER:OG 2.06 0.73

2:B:32:LEU:CD2 2:B:32:LEU:N 2.49 0.722:D:41:TYR:HE1 3:D:200:HEM:HAC 1.55 0.72

2:B:2:HIS:O 2:B:3:LEU:HD12 1.90 0.721:A:138:SER:HA 1:A:141:ARG:HH21 1.53 0.722:D:24:GLY:CA 2:D:68:ILE:HD11 2.19 0.721:C:58:HIS:HE1 3:C:200:HEM:C2A 2.09 0.71

2:B:100:PRO:HB3 2:B:142:ALA:CB 2.20 0.712:B:76:ASN:N 2:B:76:ASN:HD22 1.89 0.70

1:C:31:ARG:HG2 2:D:124:PRO:HG3 1.72 0.701:C:102:SER:O 1:C:106:LEU:HG 1.90 0.70

1:A:138:SER:HB3 1:A:139:LYS:HE2 1.72 0.702:B:87:SER:O 2:B:88:LEU:CB 2.32 0.69

1:A:113:HIS:HB3 1:A:116:ASP:OD1 1.92 0.692:B:104:ARG:HH11 2:B:104:ARG:HB2 1.57 0.692:D:104:ARG:HH11 2:D:104:ARG:HB2 1.57 0.69

2:B:4:THR:O 2:B:7:GLU:N 2.24 0.691:A:9:ASN:N 1:A:9:ASN:HD22 1.91 0.68

1:A:22:ALA:HB1 1:A:60:LYS:HG2 1.75 0.682:B:68:ILE:O 2:B:72:ASN:N 2.27 0.68





Clashoverlap (Å)

1:A:10:ILE:HG21 1:A:73:LEU:HD21 1.75 0.681:A:140:TYR:CE1 2:D:37:TRP:CE3 2.82 0.681:C:3:SER:CB 1:C:4:GLY:CA 2.67 0.68

2:D:85:PHE:HB3 2:D:141:LEU:HD23 1.75 0.681:A:127:LYS:CD 1:C:141:ARG:HG3 2.25 0.672:D:57:ASN:HD21 2:D:59:LYS:HB2 1.60 0.672:D:107:GLY:HA3 2:D:134:VAL:CG1 2.25 0.671:A:111:SER:HA 2:B:115:GLY:O 1.96 0.662:D:31:LEU:HD13 2:D:106:LEU:HA 1.76 0.662:D:29:GLY:O 2:D:33:VAL:HG23 1.94 0.66

2:B:100:PRO:HB3 2:B:142:ALA:HB1 1.77 0.662:D:94:ASP:O 2:D:95:LYS:HB3 1.96 0.651:C:58:HIS:CE1 3:C:200:HEM:C1A 2.84 0.651:C:24:TYR:CE1 1:C:112:HIS:ND1 2.61 0.651:C:40:LYS:HE2 1:C:48:VAL:HG21 1.76 0.652:B:29:GLY:O 2:B:33:VAL:HG23 1.97 0.652:B:35:TYR:O 2:B:38:THR:CG2 2.43 0.642:B:36:PRO:O 2:B:39:GLN:CG 2.37 0.642:B:105:LEU:O 2:B:109:MET:HG2 1.98 0.642:B:123:THR:HB 2:B:126:ALA:H 1.63 0.642:B:64:GLY:O 2:B:68:ILE:HG12 1.98 0.641:C:76:LEU:N 1:C:77:PRO:HD2 2.12 0.64

1:A:128:PHE:HA 1:A:131:SER:OG 1.98 0.631:C:52:SER:HB3 1:C:55:VAL:HG22 1.80 0.631:A:119:PRO:HG3 2:B:55:MET:CE 2.27 0.631:C:76:LEU:H 1:C:77:PRO:HD2 1.64 0.632:B:76:ASN:O 2:B:77:HIS:ND1 2.32 0.632:B:92:HIS:O 2:B:93:CYS:SG 2.56 0.63

2:D:3:LEU:HD12 2:D:4:THR:H 1.65 0.622:D:50:SER:O 2:D:53:ALA:N 2.32 0.622:D:93:CYS:SG 2:D:145:TYR:HA 2.40 0.62

2:D:107:GLY:HA3 2:D:134:VAL:HG13 1.82 0.621:A:84:SER:OG 1:A:139:LYS:HG2 2.00 0.612:D:142:ALA:HA 2:D:145:TYR:HD2 1.66 0.612:B:76:ASN:N 2:B:76:ASN:ND2 2.49 0.611:A:71:GLY:O 1:A:73:LEU:N 2.30 0.612:B:1:VAL:O 2:B:2:HIS:C 2.39 0.611:A:20:HIS:O 1:A:23:GLU:HG2 2.00 0.602:B:20:SER:O 2:B:68:ILE:CD1 2.44 0.602:B:28:LEU:O 2:B:32:LEU:CD2 2.50 0.60

2:D:142:ALA:HA 2:D:145:TYR:CD2 2.36 0.60Continued on next page...




Clashoverlap (Å)

1:A:9:ASN:N 1:A:9:ASN:ND2 2.48 0.602:B:104:ARG:HB2 2:B:104:ARG:NH1 2.16 0.601:A:141:ARG:NH1 1:C:1:VAL:HG21 2.16 0.591:C:17:ILE:HG23 1:C:24:TYR:CE2 2.38 0.591:C:6:ASP:O 1:C:10:ILE:HG13 2.03 0.59

2:D:24:GLY:HA3 2:D:68:ILE:CD1 2.32 0.591:A:122:HIS:ND1 2:B:30:ARG:HD3 2.17 0.581:C:83:LEU:HD21 3:C:200:HEM:HMA1 1.84 0.581:A:140:TYR:CE1 2:D:37:TRP:CZ3 2.91 0.582:B:76:ASN:HD22 2:B:76:ASN:H 1.48 0.58

1:C:10:ILE:O 1:C:14:TRP:HB2 2.02 0.581:A:90:LYS:O 1:A:90:LYS:HG2 2.03 0.58

1:C:99:LYS:HB2 1:C:99:LYS:HZ2 1.68 0.582:B:18:VAL:O 2:B:18:VAL:CG1 2.50 0.58

2:B:35:TYR:CE2 2:B:105:LEU:HG 2.39 0.582:B:92:HIS:CE1 3:B:200:HEM:C1A 2.92 0.581:A:89:HIS:CE1 1:A:139:LYS:HB3 2.39 0.572:B:146:HIS:HD2 2:B:146:HIS:O 1.88 0.562:B:90:GLU:O 2:B:94:ASP:HB3 2.06 0.56

2:B:100:PRO:HA 2:B:103:PHE:CD2 2.41 0.562:D:11:VAL:HG13 2:D:130:PHE:CZ 2.41 0.561:A:140:TYR:CE1 2:D:37:TRP:HE3 2.24 0.563:B:200:HEM:HBC2 3:B:200:HEM:HHD 1.86 0.56

1:A:6:ASP:HA 1:A:124:SER:HB3 1.88 0.552:D:40:ARG:C 2:D:41:TYR:CD2 2.80 0.552:B:18:VAL:O 2:B:19:ASN:C 2.45 0.551:A:86:LEU:O 1:A:91:LEU:N 2.40 0.55

1:A:93:VAL:HG11 1:A:98:PHE:HZ 1.72 0.552:B:15:TRP:HZ3 2:B:114:LEU:HD11 1.73 0.541:C:118:THR:HB 1:C:119:PRO:HD2 1.90 0.541:C:77:PRO:HA 1:C:135:VAL:HG13 1.89 0.542:D:31:LEU:HD22 2:D:106:LEU:HG 1.90 0.542:D:81:LEU:O 2:D:140:ALA:HB1 2.08 0.541:A:95:PRO:CG 1:A:140:TYR:OH 2.47 0.542:B:97:HIS:ND1 1:C:41:THR:HG21 2.23 0.542:B:67:VAL:HG12 2:B:68:ILE:N 2.23 0.542:D:57:ASN:ND2 2:D:59:LYS:HB2 2.22 0.541:C:36:PHE:CD2 1:C:100:LEU:HG 2.43 0.542:B:92:HIS:HE1 3:B:200:HEM:C1A 2.26 0.53

2:D:11:VAL:HG13 2:D:130:PHE:CE2 2.42 0.532:D:23:VAL:HG13 2:D:113:VAL:HG12 1.88 0.53





Clashoverlap (Å)

1:A:135:VAL:O 1:A:138:SER:HB2 2.08 0.532:B:19:ASN:O 2:B:20:SER:HB3 2.09 0.53

2:D:37:TRP:CD1 2:D:37:TRP:C 2.81 0.531:A:72:HIS:HD1 1:A:72:HIS:H 1.57 0.532:D:24:GLY:CA 2:D:68:ILE:CD1 2.86 0.531:A:15:GLY:C 1:A:17:ILE:N 2.59 0.532:D:39:GLN:HA 2:D:42:PHE:HD2 1.72 0.532:B:40:ARG:HB3 1:C:92:ARG:CD 2.39 0.531:A:58:HIS:HE1 3:A:200:HEM:C1A 2.27 0.521:C:77:PRO:HA 1:C:135:VAL:CG1 2.39 0.521:C:111:SER:HA 2:D:119:GLY:HA2 1.91 0.52

1:A:121:VAL:HG12 1:A:125:LEU:HD22 1.90 0.521:A:127:LYS:HD3 1:C:141:ARG:HG3 1.90 0.522:B:144:LYS:O 2:B:145:TYR:CD2 2.62 0.52

2:D:28:LEU:HD23 2:D:60:VAL:HG13 1.90 0.521:A:83:LEU:HD11 3:A:200:HEM:HMA3 1.90 0.521:A:86:LEU:HD12 1:A:90:LYS:HD3 1.91 0.522:D:92:HIS:HE1 3:D:200:HEM:NA 2.05 0.521:A:15:GLY:C 1:A:17:ILE:H 2.13 0.52

1:A:32:MET:HG2 1:A:39:THR:HG21 1.91 0.512:B:63:HIS:HE2 3:B:200:HEM:CHA 2.24 0.511:C:90:LYS:HG3 1:C:91:LEU:HD13 1.93 0.512:D:102:ASN:HA 2:D:105:LEU:HB2 1.91 0.511:A:17:ILE:O 1:A:20:HIS:HB2 2.10 0.51

1:A:27:GLU:OE1 1:A:108:THR:HG23 2.10 0.511:A:111:SER:O 2:B:119:GLY:HA2 2.11 0.512:D:40:ARG:O 2:D:41:TYR:CG 2.63 0.512:D:10:ALA:O 2:D:14:LEU:HB2 2.11 0.51

1:C:2:LEU:HD21 1:C:127:LYS:HB3 1.93 0.512:D:80:SER:O 2:D:82:LYS:N 2.38 0.51

1:C:94:ASP:HB3 1:C:97:ASN:OD1 2.10 0.512:B:67:VAL:HG22 3:B:200:HEM:C1B 2.45 0.502:D:72:ASN:O 2:D:75:LEU:N 2.43 0.502:D:35:TYR:O 2:D:38:THR:HB 2.11 0.501:A:24:TYR:OH 1:A:113:HIS:CE1 2.65 0.502:D:122:PHE:CZ 2:D:127:GLN:HA 2.46 0.502:B:122:PHE:CE2 2:B:127:GLN:HG3 2.47 0.501:C:3:SER:CA 1:C:6:ASP:HB2 2.42 0.50

2:D:21:ASP:OD1 2:D:22:GLU:N 2.45 0.492:D:57:ASN:HD22 2:D:59:LYS:H 1.60 0.492:B:129:ALA:O 2:B:133:VAL:HG23 2.11 0.49





Clashoverlap (Å)

2:B:31:LEU:HG 2:B:38:THR:HG21 1.94 0.492:B:100:PRO:HB3 2:B:142:ALA:HB2 1.93 0.491:C:103:HIS:HA 1:C:106:LEU:HD12 1.95 0.491:A:17:ILE:HG12 1:A:24:TYR:CD2 2.48 0.491:A:85:ASP:C 1:A:85:ASP:OD2 2.50 0.492:D:10:ALA:O 2:D:14:LEU:N 2.42 0.49

1:A:102:SER:HB2 1:A:129:LEU:HD13 1.94 0.492:D:89:SER:OG 2:D:144:LYS:HB2 2.13 0.482:B:82:LYS:H 2:B:82:LYS:HD2 1.78 0.481:A:15:GLY:O 1:A:18:GLY:N 2.44 0.481:C:79:ALA:C 1:C:81:SER:H 2.16 0.48

1:A:127:LYS:CG 1:C:141:ARG:HG3 2.43 0.482:B:40:ARG:HB3 1:C:92:ARG:HD3 1.95 0.482:D:123:THR:O 2:D:126:ALA:N 2.44 0.481:A:102:SER:HB2 1:A:129:LEU:HB3 1.96 0.482:B:146:HIS:O 2:B:146:HIS:CD2 2.66 0.47

1:C:24:TYR:HE1 1:C:112:HIS:CG 2.32 0.472:B:14:LEU:HD12 2:B:14:LEU:HA 1.68 0.472:B:70:ALA:HA 2:B:73:ASP:OD2 2.14 0.472:B:97:HIS:CG 1:C:41:THR:HG21 2.50 0.472:D:123:THR:O 2:D:127:GLN:N 2.39 0.471:A:22:ALA:CB 1:A:60:LYS:HE2 2.44 0.471:C:45:HIS:ND1 1:C:45:HIS:N 2.55 0.471:A:94:ASP:O 1:A:97:ASN:OD1 2.33 0.47

1:A:140:TYR:HE1 2:D:37:TRP:CZ3 2.32 0.471:A:10:ILE:HD13 1:A:128:PHE:HB2 1.97 0.471:C:3:SER:H 1:C:6:ASP:HB2 1.80 0.47

1:C:107:VAL:HG11 2:D:127:GLN:OE1 2.15 0.472:B:65:LYS:O 2:B:68:ILE:HG13 2.15 0.47

1:C:66:LEU:HD21 3:C:200:HEM:HBB2 1.97 0.461:A:9:ASN:ND2 1:A:9:ASN:H 2.13 0.462:B:28:LEU:O 2:B:32:LEU:HD23 2.15 0.46

1:C:137:THR:HA 1:C:140:TYR:CE2 2.50 0.462:D:48:LEU:O 2:D:54:ILE:HG12 2.15 0.462:B:77:HIS:HE1 4:B:155:HOH:O 1.97 0.461:A:17:ILE:HG12 1:A:24:TYR:CE2 2.51 0.461:A:31:ARG:HD3 2:B:127:GLN:OE1 2.14 0.461:C:76:LEU:N 1:C:77:PRO:CD 2.79 0.462:D:40:ARG:O 2:D:41:TYR:CD2 2.68 0.46

2:D:76:ASN:OD1 2:D:76:ASN:N 2.48 0.462:D:127:GLN:CG 2:D:128:ALA:N 2.78 0.46





Clashoverlap (Å)

1:A:48:VAL:HG12 1:A:48:VAL:O 2.15 0.462:B:68:ILE:C 2:B:71:PHE:H 2.19 0.46

2:D:45:PHE:CE1 2:D:59:LYS:HB3 2.50 0.461:A:83:LEU:HD11 3:A:200:HEM:CMA 2.45 0.462:B:26:GLU:OE1 2:B:113:VAL:HG13 2.16 0.462:B:146:HIS:CD2 2:B:146:HIS:C 2.89 0.461:C:17:ILE:HG23 1:C:24:TYR:HE2 1.80 0.461:C:22:ALA:HB1 1:C:60:LYS:HB2 1.98 0.461:C:35:SER:HA 2:D:128:ALA:CB 2.46 0.462:B:23:VAL:O 2:B:27:ALA:N 2.43 0.451:C:37:PRO:O 1:C:40:LYS:HB2 2.17 0.451:C:42:TYR:O 3:C:200:HEM:CMD 2.65 0.451:A:121:VAL:O 1:A:122:HIS:C 2.54 0.451:C:113:HIS:N 1:C:114:PRO:HD3 2.31 0.45

2:D:41:TYR:CE1 3:D:200:HEM:HAC 2.42 0.452:D:45:PHE:CD1 2:D:59:LYS:HB3 2.52 0.451:A:80:LEU:HB2 1:A:135:VAL:HG11 1.99 0.452:B:18:VAL:O 2:B:18:VAL:HG12 2.17 0.45

2:D:34:VAL:HG23 2:D:35:TYR:CE2 2.50 0.451:A:72:HIS:O 1:A:76:LEU:HD13 2.16 0.45

1:A:140:TYR:HE1 2:D:37:TRP:HZ3 1.63 0.452:B:114:LEU:O 2:B:118:LEU:HB2 2.18 0.442:D:3:LEU:HB3 2:D:8:LYS:HB2 1.99 0.441:C:3:SER:OG 1:C:4:GLY:HA2 2.16 0.44

2:D:107:GLY:CA 2:D:134:VAL:HG13 2.46 0.441:A:15:GLY:O 1:A:17:ILE:N 2.51 0.441:A:116:ASP:O 1:A:118:THR:N 2.49 0.441:C:98:PHE:CE2 1:C:137:THR:CG2 3.01 0.442:D:82:LYS:N 2:D:82:LYS:HD2 2.33 0.44

1:A:42:TYR:OH 1:A:94:ASP:HB2 2.18 0.441:A:31:ARG:HA 2:B:124:PRO:HB3 1.99 0.441:C:140:TYR:N 1:C:140:TYR:CD2 2.86 0.442:D:24:GLY:H 2:D:68:ILE:HD11 1.79 0.44

2:D:100:PRO:HD3 2:D:145:TYR:CZ 2.50 0.441:A:8:SER:O 1:A:12:ALA:CB 2.66 0.44

1:A:35:SER:HB2 1:A:36:PHE:CE2 2.52 0.442:D:33:VAL:HG22 2:D:54:ILE:HD12 2.00 0.442:D:94:ASP:O 2:D:95:LYS:CB 2.65 0.44

2:D:106:LEU:HD12 3:D:200:HEM:CHC 2.48 0.443:D:200:HEM:HBA1 3:D:200:HEM:CMA 2.48 0.44

2:B:28:LEU:O 2:B:31:LEU:HB3 2.18 0.43Continued on next page...




Clashoverlap (Å)

1:C:24:TYR:O 1:C:25:GLY:C 2.57 0.431:C:86:LEU:O 1:C:91:LEU:HB2 2.18 0.432:B:73:ASP:O 2:B:77:HIS:HB2 2.18 0.431:C:35:SER:HA 2:D:128:ALA:HB1 2.00 0.431:C:54:GLN:HB2 4:C:142:HOH:O 2.19 0.432:B:22:GLU:O 2:B:26:GLU:HB2 2.18 0.43

1:C:93:VAL:CG1 3:C:200:HEM:HBC2 2.49 0.432:B:68:ILE:O 2:B:69:THR:C 2.56 0.431:C:3:SER:N 1:C:6:ASP:HB2 2.34 0.43

2:B:20:SER:HB3 4:B:149:HOH:O 2.18 0.431:C:24:TYR:HH 1:C:113:HIS:HE2 1.65 0.431:C:47:ASP:OD2 1:C:47:ASP:C 2.57 0.431:A:87:HIS:HA 1:A:91:LEU:HB2 2.01 0.431:A:37:PRO:O 1:A:40:LYS:HB2 2.19 0.432:D:98:VAL:O 2:D:145:TYR:HE1 2.02 0.42

2:B:40:ARG:HB3 1:C:92:ARG:HD2 2.01 0.421:C:3:SER:HA 1:C:6:ASP:HB2 2.00 0.42

2:D:57:ASN:ND2 2:D:59:LYS:H 2.16 0.421:C:42:TYR:CE1 1:C:93:VAL:HA 2.55 0.422:D:41:TYR:CD2 2:D:41:TYR:N 2.88 0.421:A:69:ALA:HB2 1:A:80:LEU:HD21 2.00 0.422:B:99:ASP:HA 2:B:100:PRO:HD3 1.77 0.422:B:92:HIS:O 2:B:93:CYS:CB 2.68 0.421:C:9:ASN:HA 1:C:12:ALA:HB3 2.01 0.422:B:39:GLN:HA 2:B:42:PHE:HD2 1.84 0.422:B:103:PHE:HD1 3:B:200:HEM:HBB2 1.85 0.422:B:24:GLY:H 2:B:68:ILE:HD13 1.85 0.41

2:D:107:GLY:CA 2:D:134:VAL:CG1 2.96 0.412:B:36:PRO:C 2:B:38:THR:H 2.23 0.412:B:92:HIS:HE1 3:B:200:HEM:NA 2.01 0.412:B:130:PHE:HA 2:B:133:VAL:HB 2.02 0.411:C:81:SER:HA 1:C:84:SER:HB2 2.01 0.41

2:D:23:VAL:HG13 2:D:113:VAL:CG1 2.51 0.412:D:74:GLY:O 2:D:77:HIS:N 2.53 0.411:A:58:HIS:HE1 3:A:200:HEM:CHA 2.33 0.411:C:66:LEU:O 1:C:69:ALA:HB3 2.20 0.41

1:A:137:THR:HG22 1:A:137:THR:O 2.20 0.412:D:99:ASP:HA 2:D:100:PRO:HD2 1.79 0.412:B:45:PHE:N 2:B:45:PHE:CD2 2.89 0.411:C:117:PHE:O 2:D:30:ARG:NH2 2.51 0.411:A:27:GLU:O 1:A:31:ARG:HG3 2.21 0.41





Clashoverlap (Å)

1:A:58:HIS:CE1 3:A:200:HEM:CHA 3.04 0.412:D:63:HIS:CE1 2:D:67:VAL:HG23 2.56 0.411:C:97:ASN:HA 1:C:100:LEU:HB2 2.03 0.411:A:95:PRO:O 1:A:98:PHE:HD2 2.03 0.40

1:A:137:THR:HG23 1:A:140:TYR:OH 2.21 0.402:B:132:LYS:HE3 2:B:132:LYS:HB2 1.58 0.401:C:42:TYR:CD2 3:C:200:HEM:HBC1 2.57 0.401:C:49:SER:O 1:C:50:HIS:C 2.59 0.40

1:C:66:LEU:HD21 3:C:200:HEM:CBB 2.50 0.401:C:123:ALA:HA 2:D:34:VAL:HG12 2.03 0.401:A:141:ARG:NH2 1:C:1:VAL:HG11 2.37 0.401:C:97:ASN:O 1:C:100:LEU:HB2 2.22 0.40

3:D:200:HEM:HBA1 3:D:200:HEM:HMA1 2.03 0.401:A:6:ASP:OD2 1:A:127:LYS:CE 2.50 0.401:C:59:GLY:O 1:C:62:VAL:HB 2.21 0.401:C:97:ASN:HA 1:C:100:LEU:HD22 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 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 139/141 (99%) 123 (88%) 13 (9%) 3 (2%) 6 22

1 C 139/141 (99%) 127 (91%) 10 (7%) 2 (1%) 11 34

2 B 144/146 (99%) 121 (84%) 17 (12%) 6 (4%) 3 9

2 D 144/146 (99%) 124 (86%) 14 (10%) 6 (4%) 3 9

All All 566/574 (99%) 495 (88%) 54 (10%) 17 (3%) 4 15

All (17) Ramachandran outliers are listed below:

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

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


Mol Chain Res Type1 A 4 GLY2 B 77 HIS2 B 93 CYS2 D 81 LEU2 D 95 LYS1 A 72 HIS2 B 19 ASN2 B 20 SER2 B 47 ASP1 A 16 LYS2 D 21 ASP2 D 121 ASP1 C 3 SER1 C 2 LEU2 B 88 LEU2 D 119 GLY2 D 100 PRO

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 110/110 (100%) 90 (82%) 20 (18%) 1 5

1 C 110/110 (100%) 92 (84%) 18 (16%) 2 7

2 B 115/115 (100%) 91 (79%) 24 (21%) 1 3

2 D 115/115 (100%) 91 (79%) 24 (21%) 1 3

All All 450/450 (100%) 364 (81%) 86 (19%) 1 4

All (86) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 9 ASN1 A 17 ILE1 A 38 THR1 A 41 THR1 A 45 HIS


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


Continued from previous page...Mol Chain Res Type1 A 47 ASP1 A 60 LYS1 A 72 HIS1 A 74 ASP1 A 76 LEU1 A 85 ASP1 A 92 ARG1 A 94 ASP1 A 102 SER1 A 111 SER1 A 116 ASP1 A 125 LEU1 A 128 PHE1 A 131 SER1 A 141 ARG2 B 4 THR2 B 8 LYS2 B 11 VAL2 B 14 LEU2 B 18 VAL2 B 26 GLU2 B 32 LEU2 B 40 ARG2 B 44 SER2 B 76 ASN2 B 77 HIS2 B 79 ASP2 B 80 SER2 B 81 LEU2 B 82 LYS2 B 88 LEU2 B 91 LEU2 B 106 LEU2 B 111 VAL2 B 118 LEU2 B 123 THR2 B 132 LYS2 B 145 TYR2 B 146 HIS1 C 7 LYS1 C 9 ASN1 C 23 GLU



Continued from previous page...Mol Chain Res Type1 C 35 SER1 C 45 HIS1 C 47 ASP1 C 60 LYS1 C 76 LEU1 C 83 LEU1 C 84 SER1 C 91 LEU1 C 99 LYS1 C 100 LEU1 C 101 LEU1 C 105 LEU1 C 124 SER1 C 125 LEU1 C 140 TYR2 D 2 HIS2 D 13 CYS2 D 20 SER2 D 21 ASP2 D 26 GLU2 D 28 LEU2 D 38 THR2 D 41 TYR2 D 43 ASP2 D 57 ASN2 D 75 LEU2 D 76 ASN2 D 80 SER2 D 81 LEU2 D 82 LYS2 D 87 SER2 D 88 LEU2 D 94 ASP2 D 104 ARG2 D 106 LEU2 D 118 LEU2 D 120 LYS2 D 127 GLN2 D 146 HIS

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (17)such sidechains are listed below:


Mol Chain Res Type1 A 9 ASN1 A 50 HIS1 A 58 HIS1 A 103 HIS1 A 113 HIS2 B 39 GLN2 B 76 ASN2 B 102 ASN2 B 108 ASN2 B 131 GLN2 B 146 HIS1 C 9 ASN1 C 58 HIS2 D 57 ASN2 D 63 HIS2 D 116 HIS2 D 131 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○

4 ligands are 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 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).

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

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




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

3 HEM A 200 4,1 27,50,50 2.26 6 (22%) 17,82,82 1.58 5 (29%)3 HEM D 200 4,2 27,50,50 2.29 6 (22%) 17,82,82 1.54 2 (11%)3 HEM B 200 2 27,50,50 2.20 5 (18%) 17,82,82 1.74 4 (23%)3 HEM C 200 4,1 27,50,50 2.17 6 (22%) 17,82,82 1.71 4 (23%)

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 HEM A 200 4,1 - 0/6/54/54 -3 HEM D 200 4,2 - 5/6/54/54 -3 HEM B 200 2 - 2/6/54/54 -3 HEM C 200 4,1 - 4/6/54/54 -

All (23) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)3 B 200 HEM C3B-C2B -5.30 1.33 1.403 D 200 HEM C3D-C2D 5.29 1.53 1.373 A 200 HEM C3B-C2B -5.27 1.33 1.403 A 200 HEM C3D-C2D 5.26 1.53 1.373 B 200 HEM C3D-C2D 5.17 1.53 1.373 A 200 HEM C3C-C2C -5.07 1.33 1.403 D 200 HEM C3B-C2B -5.04 1.33 1.403 C 200 HEM C3D-C2D 4.94 1.52 1.373 D 200 HEM C3C-CAC 4.68 1.57 1.473 C 200 HEM C3B-C2B -4.60 1.34 1.403 B 200 HEM C3C-C2C -4.60 1.34 1.403 D 200 HEM C3C-C2C -4.28 1.34 1.403 C 200 HEM C3C-C2C -4.24 1.34 1.403 B 200 HEM C3C-CAC 4.02 1.56 1.473 C 200 HEM C3C-CAC 3.67 1.55 1.473 A 200 HEM C3C-CAC 3.53 1.55 1.473 C 200 HEM C3B-CAB 3.52 1.55 1.473 D 200 HEM C3B-CAB 3.47 1.55 1.473 C 200 HEM CAA-C2A 3.37 1.57 1.523 B 200 HEM C3B-CAB 3.32 1.54 1.473 A 200 HEM C3B-CAB 3.00 1.54 1.473 A 200 HEM CAA-C2A 2.42 1.55 1.52



Continued from previous page...Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)3 D 200 HEM CAD-C3D 2.17 1.56 1.52

All (15) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)3 B 200 HEM CBD-CAD-C3D -4.17 104.79 112.483 C 200 HEM CMA-C3A-C4A -4.16 122.08 128.463 D 200 HEM CMA-C3A-C4A -4.04 122.25 128.463 A 200 HEM CBD-CAD-C3D -3.14 106.69 112.483 C 200 HEM CBD-CAD-C3D -3.08 106.80 112.483 B 200 HEM CAA-CBA-CGA -2.94 107.75 112.673 B 200 HEM CMA-C3A-C4A -2.86 124.06 128.463 A 200 HEM C1D-C2D-C3D -2.83 105.03 107.003 A 200 HEM CBA-CAA-C2A 2.65 117.37 112.493 C 200 HEM C4A-C3A-C2A 2.63 108.83 107.003 D 200 HEM CMA-C3A-C2A 2.55 129.75 124.943 A 200 HEM CAA-CBA-CGA -2.36 108.71 112.673 C 200 HEM CMA-C3A-C2A 2.20 129.09 124.943 A 200 HEM CAD-CBD-CGD -2.12 109.12 112.673 B 200 HEM C3C-C4C-NC -2.04 107.09 110.94

There are no chirality outliers.

All (11) torsion outliers are listed below:

Mol Chain Res Type Atoms3 B 200 HEM C2A-CAA-CBA-CGA3 C 200 HEM C1A-C2A-CAA-CBA3 C 200 HEM C3A-C2A-CAA-CBA3 C 200 HEM C3D-CAD-CBD-CGD3 D 200 HEM C1A-C2A-CAA-CBA3 D 200 HEM C3A-C2A-CAA-CBA3 D 200 HEM C2D-C3D-CAD-CBD3 D 200 HEM C4D-C3D-CAD-CBD3 D 200 HEM C3D-CAD-CBD-CGD3 B 200 HEM C3D-CAD-CBD-CGD3 C 200 HEM C2A-CAA-CBA-CGA

There are no ring outliers.

4 monomers are involved in 31 short contacts:


Mol Chain Res Type Clashes Symm-Clashes3 A 200 HEM 8 03 D 200 HEM 7 03 B 200 HEM 7 03 C 200 HEM 9 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.


Ligand HEM A 200

Bond lengths Bond angles

Torsions Rings


Ligand HEM D 200


Torsions Rings


Ligand HEM B 200


Torsions Rings


Ligand HEM C 200


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/XrayValidationReportHelp#polymer_linkage


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 141/141 (100%) -0.22 4 (2%) 53 43 22, 34, 49, 53 0

1 C 141/141 (100%) -0.08 5 (3%) 44 34 20, 38, 64, 68 0

2 B 146/146 (100%) -0.20 4 (2%) 54 44 15, 34, 51, 56 0

2 D 146/146 (100%) -0.20 5 (3%) 45 35 21, 33, 53, 65 0

All All 574/574 (100%) -0.17 18 (3%) 49 39 15, 34, 56, 68 0

All (18) RSRZ outliers are listed below:

Mol Chain Res Type RSRZ2 B 146 HIS 7.51 A 141 ARG 4.62 B 2 HIS 4.22 B 145 TYR 3.92 D 2 HIS 3.71 A 20 HIS 3.51 C 19 GLY 3.31 A 140 TYR 3.02 D 5 ASP 3.02 B 93 CYS 3.02 D 4 THR 3.01 C 75 ASP 2.61 C 1 VAL 2.52 D 6 ALA 2.52 D 146 HIS 2.41 C 138 SER 2.31 C 141 ARG 2.31 A 72 HIS 2.2

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_model_data

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_protein_na_chains


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 monosaccharides 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<0.93 HEM D 200 43/43 0.87 0.23 20,23,30,32 03 HEM A 200 43/43 0.91 0.22 27,28,32,33 03 HEM B 200 43/43 0.92 0.18 32,34,36,40 03 HEM C 200 43/43 0.93 0.17 27,33,42,44 0

The following is a graphical depiction of the model fit to experimental electron density of allinstances of the Ligand of Interest. In addition, ligands with molecular weight > 250 and outliersas shown on the geometry validation Tables will also be included. Each fit is shown from differentorientation to approximate a three-dimensional view.

https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#fit_nonstandard_and_ligands




Electron density around HEM D 200:

2mFo-DFc (at 0.7 rmsd) in graymFo-DFc (at 3 rmsd) in purple (negative)

and green (positive)


Electron density around HEM A 200:




Electron density around HEM B 200:




Electron density around HEM C 200:



6.5 Other polymers i○

There are no such residues in this entry.


full wwpdb x-ray structure validation report i

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