Full wwPDB X-ray Structure Validation Report i○

Mar 18, 2019 – 10:14 PM EDT

PDB ID : 6CVCTitle : Mycobacterium marinum cytochrome P450 CYP124A1 in the substrate-free

formAuthors : Child, S.A.; Bruning, J.B.; Bell, S.G.

Deposited on : 2018-03-27Resolution : 2.20 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 : 1.8.0 (224370), CSD as540be (2019)

Xtriage (Phenix) : 1.13EDS : rb-20031633

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) : rb-20031633

Page 2 Full wwPDB X-ray Structure Validation Report 6CVC

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 2.20 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 4343 (2.20-2.20)Clashscore 122126 5027 (2.20-2.20)

Ramachandran outliers 120053 4952 (2.20-2.20)Sidechain outliers 120020 4953 (2.20-2.20)RSRZ outliers 108989 4245 (2.20-2.20)

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 433

Page 3 Full wwPDB X-ray Structure Validation Report 6CVC

2 Entry composition i○

There are 4 unique types of molecules in this entry. The entry contains 3718 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 Cytochrome P450 124A1, Cyp124A1.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 422 Total C N O S3363 2125 598 627 13 0 5 0

There are 10 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA -3 MET - initiating methionine UNP B2HHT9A -2 ASP - expression tag UNP B2HHT9A -1 LEU - expression tag UNP B2HHT9A 0 SER - expression tag UNP B2HHT9A 1 THR - expression tag UNP B2HHT9A 2 ASN - expression tag UNP B2HHT9A 3 LEU - expression tag UNP B2HHT9A 4 ASN - expression tag UNP B2HHT9A 5 THR - expression tag UNP B2HHT9A 6 GLY - expression tag UNP B2HHT9

• Molecule 2 is PROTOPORPHYRIN IX CONTAINING FE (three-letter code: HEM) (for-mula: C34H32FeN4O4).

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

Mol Chain Residues Atoms ZeroOcc AltConf

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

• Molecule 3 is SULFATE ION (three-letter code: SO4) (formula: O4S).

Mol Chain Residues Atoms ZeroOcc AltConf

3 A 1 Total O S5 4 1 0 0

3 A 1 Total O S5 4 1 0 0

3 A 1 Total O S5 4 1 0 0

Page 5 Full wwPDB X-ray Structure Validation Report 6CVC

• Molecule 4 is water.

Mol Chain Residues Atoms ZeroOcc AltConf

4 A 297 Total O297 297 0 0

Page 6 Full wwPDB X-ray Structure Validation Report 6CVC

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: Cytochrome P450 124A1, Cyp124A1

Chain A:

MET

ASP

LEU

SER

THR

ASN

LEU

ASN

THR

GLY

L7•

W32

R48

E49

I52

S53

F54

W55

L60•

A61•

G62•

L63•

T64•

A65•

K74

I78

E86

I87

I96

Q99

R120

R127

V141

L171

P172

I175

D202•

L205•

T206•

T207•

D208•

E250

W294

Y317

M318

R319

L322

V326

D327

L328

R329

M333

L341

W342

A346

R398

Q415

R422

S428

ARG

Page 7 Full wwPDB X-ray Structure Validation Report 6CVC

4 Data and refinement statistics i○

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

98.78Å 72.36Å 65.60Å90.00◦ 109.72◦ 90.00◦ Depositor

Resolution (Å) 25.19 – 2.2025.19 – 2.20

DepositorEDS

% Data completeness(in resolution range)

98.8 (25.19-2.20)98.8 (25.19-2.20)

DepositorEDS

Rmerge 0.30 DepositorRsym (Not available) Depositor

< I/σ(I) > 1 1.67 (at 2.19Å) XtriageRefinement program PHENIX 1.11.1_2575 Depositor

R, Rfree0.204 , 0.2540.204 , 0.254

DepositorDCC

Rfree test set 1070 reflections (4.88%) wwPDB-VPWilson B-factor (Å2) 19.4 Xtriage

Anisotropy 0.139 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.34 , 48.4 EDS

L-test for twinning2 < |L| > = 0.49, < L2 > = 0.32 XtriageEstimated twinning fraction No twinning to report. Xtriage

Fo,Fc correlation 0.93 EDSTotal number of atoms 3718 wwPDB-VP

Average B, all atoms (Å2) 29.0 wwPDB-VP

Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Pattersonfunction is 6.18% 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 8 Full wwPDB X-ray Structure Validation Report 6CVC

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, SO4

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 0.23 0/3450 0.39 0/4694

There are no bond length outliers.

There are no bond angle outliers.

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 3363 0 3256 19 02 A 43 0 30 2 03 A 15 0 0 0 04 A 297 0 0 2 0All All 3718 0 3286 21 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 3.

All (21) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

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Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:A:78:ILE:HD12 1:A:346:ALA:HB2 1.81 0.631:A:52:ILE:HD13 1:A:328:LEU:HD13 1.82 0.611:A:7:LEU:N 4:A:606:HOH:O 2.35 0.60

1:A:86:GLU:HG2 1:A:87:ILE:HG13 1.86 0.572:A:501:HEM:HBC2 2:A:501:HEM:HMC1 1.90 0.541:A:78:ILE:HG23 1:A:341:LEU:HB3 1.90 0.531:A:422:ARG:NH1 4:A:604:HOH:O 2.33 0.532:A:501:HEM:HMB2 2:A:501:HEM:HBB2 1.92 0.521:A:141:VAL:HG22 1:A:175:ILE:HD13 1.92 0.521:A:53:SER:HG 1:A:55:TRP:HE1 1.62 0.47

1:A:120:ARG:NH2 1:A:250:GLU:OE1 2.44 0.461:A:322:LEU:HD11 1:A:333:MET:HE3 1.99 0.45

1:A:63:LEU:H 1:A:63:LEU:HD23 1.80 0.451:A:74:LYS:HE2 1:A:329:ARG:HH12 1.81 0.441:A:96:ILE:HG13 1:A:317:TYR:CE2 2.53 0.431:A:48:ARG:NH2 1:A:49:GLU:OE1 2.50 0.431:A:317:TYR:HB3 1:A:342:TRP:CE3 2.55 0.411:A:32:TRP:CZ2 1:A:415:GLN:HG3 2.55 0.41

1:A:326:VAL:HG12 1:A:328:LEU:HG 2.03 0.411:A:53:SER:OG 1:A:55:TRP:NE1 2.53 0.411:A:171:LEU:HB3 1:A:172:PRO:HD3 2.02 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 425/433 (98%) 418 (98%) 7 (2%) 0 100 100

There are no Ramachandran outliers to report.

Page 10 Full wwPDB X-ray Structure Validation Report 6CVC

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 357/362 (99%) 349 (98%) 8 (2%) 55 68

All (8) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 99 GLN1 A 120 ARG1 A 127 ARG1 A 205 LEU1 A 294 TRP1 A 319 ARG1 A 328 LEU1 A 398 ARG

Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. There are nosuch sidechains identified.

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 carbohydrates in this entry.

5.6 Ligand geometry i○

4 ligands are modelled in this entry.

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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 HEM A 501 1,4 27,50,50 1.80 4 (14%) 17,82,82 1.50 3 (17%)3 SO4 A 502 - 4,4,4 0.16 0 6,6,6 0.06 03 SO4 A 503 - 4,4,4 0.16 0 6,6,6 0.04 03 SO4 A 504 - 4,4,4 0.16 0 6,6,6 0.05 0

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 HEM A 501 1,4 - 0/6/54/54 0/0/8/83 SO4 A 502 - - 0/0/0/0 0/0/0/03 SO4 A 503 - - 0/0/0/0 0/0/0/03 SO4 A 504 - - 0/0/0/0 0/0/0/0

All (4) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)2 A 501 HEM C3B-C2B -3.80 1.35 1.402 A 501 HEM C3C-C2C -3.60 1.35 1.402 A 501 HEM C3B-CAB 3.80 1.55 1.472 A 501 HEM C3C-CAC 3.81 1.55 1.47

All (3) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 A 501 HEM CMA-C3A-C4A -2.08 125.27 128.462 A 501 HEM CMC-C2C-C3C 2.17 128.88 124.802 A 501 HEM CMB-C2B-C3B 2.29 129.09 124.80

There are no chirality outliers.

There are no torsion outliers.

Page 12 Full wwPDB X-ray Structure Validation Report 6CVC

There are no ring outliers.

1 monomer is involved in 2 short contacts:

Mol Chain Res Type Clashes Symm-Clashes2 A 501 HEM 2 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 13 Full wwPDB X-ray Structure Validation Report 6CVC

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 422/433 (97%) 0.13 12 (2%) 53 50 14, 26, 54, 86 0

All (12) RSRZ outliers are listed below:

Mol Chain Res Type RSRZ1 A 64 THR 5.41 A 63 LEU 5.31 A 205 LEU 4.11 A 60 LEU 3.91 A 61 ALA 3.41 A 65 ALA 3.21 A 206 THR 3.11 A 62 GLY 2.71 A 208 ASP 2.51 A 207 THR 2.41 A 7 LEU 2.31 A 202 ASP 2.2

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,

Page 14 Full wwPDB X-ray Structure Validation Report 6CVC

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 SO4 A 504 5/5 0.92 0.17 66,68,69,69 03 SO4 A 503 5/5 0.96 0.16 47,52,56,56 03 SO4 A 502 5/5 0.97 0.15 39,43,45,46 02 HEM A 501 43/43 0.97 0.11 4,12,19,22 0

6.5 Other polymers i○

There are no such residues in this entry.