Full wwPDB X-ray Structure Validation Report iO

Aug 9, 2020 � 01:54 AM BST

PDB ID : 6VTBTitle : Naegleria gruberi RNA ligase K326A mutant with ATP and Mn

Authors : Unciuleac, M.C.; Goldgur, Y.; Shuman, S.Deposited on : 2020-02-12Resolution : 1.55 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 speci�c help available everywhere you see the iO symbol.

The following versions of software and data (see references iO) were used in the production of this report:

MolProbity : 4.02b-467Mogul : 1.8.5 (274361), CSD as541be (2020)

Xtriage (Phenix) : 1.13EDS : 2.13.1

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) : 2.13.1

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

1 Overall quality at a glance iO

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

The reported resolution of this entry is 1.55 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.

MetricWhole archive(#Entries)

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

Rfree 130704 2556 (1.56-1.52)Clashscore 141614 2634 (1.56-1.52)

Ramachandran outliers 138981 2580 (1.56-1.52)Sidechain outliers 138945 2577 (1.56-1.52)RSRZ outliers 127900 2524 (1.56-1.52)

The table below summarises the geometric issues observed across the polymeric chains and their�t to the electron density. The red, orange, yellow and green segments on 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 �t to the electron density. The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 A 340

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2 Entry composition iO

There are 4 unique types of molecules in this entry. The entry contains 3450 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 RNA ligase.

Mol Chain Residues Atoms ZeroOcc AltConf Trace

1 A 340Total C N O S2713 1707 479 517 10

0 0 0

There are 2 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 0 SER - expression tag UNP D2W2Z5A 326 ALA LYS engineered mutation UNP D2W2Z5

� Molecule 2 is ADENOSINE-5'-TRIPHOSPHATE (three-letter code: ATP) (formula:C10H16N5O13P3) (labeled as "Ligand of Interest" by author).

Mol Chain Residues Atoms ZeroOcc AltConf

2 A 1Total C N O P31 10 5 13 3

0 0

� Molecule 3 is MANGANESE (II) ION (three-letter code: MN) (formula: Mn) (labeled as

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"Ligand of Interest" by author).

Mol Chain Residues Atoms ZeroOcc AltConf

3 A 3Total Mn3 3

0 0

� Molecule 4 is water.

Mol Chain Residues Atoms ZeroOcc AltConf

4 A 703Total O703 703

0 0

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3 Residue-property plots iO

These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The�rst 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 �t 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: RNA ligase

Chain A:

S0

R10

A19•

G20•

A21•

E22•

A23•

H28

V29

D30

T33

D53

N60

Q76

R100

K121

T128•

R149

I154

P155

K164

I185

R208

N209

K210

M211

I212

K241

G242

Q243

D249

T277

R339

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4 Data and re�nement statistics iO

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

53.03Å 64.22Å 101.89Å90.00◦ 90.00◦ 90.00◦

Depositor

Resolution (Å)28.60 � 1.5528.60 � 1.55

DepositorEDS

% Data completeness(in resolution range)

95.8 (28.60-1.55)90.7 (28.60-1.55)

DepositorEDS

Rmerge 0.11 DepositorRsym (Not available) Depositor

< I/σ(I) > 1 1.60 (at 1.54Å) XtriageRe�nement program PHENIX 1.16_3549 Depositor

R, Rfree0.163 , 0.1950.163 , 0.194

DepositorDCC

Rfree test set 1981 re�ections (4.02%) wwPDB-VPWilson B-factor (Å2) 10.7 Xtriage

Anisotropy 0.343 XtriageBulk solvent ksol(e/Å3), Bsol(Å2) 0.30 , 43.8 EDS

L-test for twinning2 < |L| > = 0.48, < L2 > = 0.32 XtriageEstimated twinning fraction No twinning to report. Xtriage

Fo,Fc correlation 0.96 EDSTotal number of atoms 3450 wwPDB-VP

Average B, all atoms (Å2) 17.0 wwPDB-VP

Xtriage's analysis on translational NCS is as follows: The largest o�-origin peak in the Patterson

function is 5.48% of the height of the origin peak. No signi�cant pseudotranslation is detected.

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

and 0.375, 0.2 for perfectly twinned datasets.

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5 Model quality iO

5.1 Standard geometry iO

Bond lengths and bond angles in the following residue types are not validated in this section: MN,ATP

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 ChainBond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >5

1 A 0.34 0/2760 0.56 0/3718

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 iO

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 2713 0 2706 16 02 A 31 0 12 0 03 A 3 0 0 0 04 A 703 0 0 6 0All All 3450 0 2718 16 0

The all-atom clashscore is de�ned as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 3.

All (16) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

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Atom-1 Atom-2Interatomicdistance (Å)

Clashoverlap (Å)

1:A:76:GLN:NE2 4:A:501:HOH:O 2.10 0.841:A:60:ASN:ND2 4:A:512:HOH:O 2.37 0.571:A:0:SER:OG 1:A:121:LYS:NZ 2.38 0.571:A:241:LYS:NZ 4:A:517:HOH:O 2.42 0.531:A:53:ASP:OD2 1:A:149:ARG:NH2 2.43 0.521:A:208:ARG:NH2 1:A:243:GLN:O 2.45 0.491:A:28:HIS:CD2 1:A:33:THR:HG22 2.50 0.471:A:149:ARG:NE 4:A:520:HOH:O 2.50 0.451:A:210:LYS:HB3 1:A:210:LYS:HE2 1.56 0.441:A:209:ASN:HB2 1:A:277:THR:O 2.18 0.431:A:164:LYS:HB2 1:A:164:LYS:HE3 1.79 0.431:A:10:ARG:HD3 1:A:30:ASP:OD2 2.20 0.411:A:154:ILE:HB 1:A:155:PRO:HD3 2.02 0.411:A:185:ILE:HG21 1:A:212:ILE:HG23 2.02 0.411:A:100:ARG:NH1 4:A:539:HOH:O 2.51 0.411:A:149:ARG:NH1 4:A:502:HOH:O 2.14 0.40

There are no symmetry-related clashes.

5.3 Torsion angles iO

5.3.1 Protein backbone iO

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 338/340 (99%) 332 (98%) 6 (2%) 0 100 100

There are no Ramachandran outliers to report.

5.3.2 Protein sidechains iO

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 was

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analysed, and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles

1 A 293/293 (100%) 292 (100%) 1 (0%) 92 84

All (1) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 249 ASP

Some sidechains can be �ipped to improve hydrogen bonding and reduce clashes. All (1) suchsidechains are listed below:

Mol Chain Res Type1 A 60 ASN

5.3.3 RNA iO

There are no RNA molecules in this entry.

5.4 Non-standard residues in protein, DNA, RNA chains iO

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

5.5 Carbohydrates iO

There are no monosaccharides in this entry.

5.6 Ligand geometry iO

Of 4 ligands modelled in this entry, 3 are monoatomic - leaving 1 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 de�ned 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).

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Mol Type Chain Res LinkBond lengths Bond angles

Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

2 ATP A 401 3 26,33,33 1.11 3 (11%) 31,52,52 1.37 4 (12%)

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 de�ned in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.'-' means no outliers of that kind were identi�ed.

Mol Type Chain Res Link Chirals Torsions Rings2 ATP A 401 3 - 3/18/38/38 0/3/3/3

All (3) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)2 A 401 ATP O4'-C1' 3.37 1.45 1.412 A 401 ATP C2-N3 2.36 1.35 1.322 A 401 ATP C5-C4 2.20 1.46 1.40

All (4) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)2 A 401 ATP N3-C2-N1 -3.17 123.73 128.682 A 401 ATP C3'-C2'-C1' 2.71 105.05 100.982 A 401 ATP O3G-PG-O3B 2.13 111.79 104.642 A 401 ATP PB-O3B-PG -2.12 125.57 132.83

There are no chirality outliers.

All (3) torsion outliers are listed below:

Mol Chain Res Type Atoms2 A 401 ATP PB-O3B-PG-O3G2 A 401 ATP C4'-C5'-O5'-PA2 A 401 ATP PB-O3B-PG-O1G

There are no ring outliers.

No monomer is involved in short contacts.

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.

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Any bond that is central to one or more torsion angles identi�ed 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 identi�ed 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-identi�ed 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 �nd su�cientequivalents in the CSD to analyse the geometry.

Ligand ATP A 401

Bond lengths Bond angles

Torsions Rings

5.7 Other polymers iO

There are no such residues in this entry.

5.8 Polymer linkage issues iO

There are no chain breaks in this entry.

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6 Fit of model and data iO

6.1 Protein, DNA and RNA chains iO

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 340/340 (100%) -0.30 6 (1%) 68 74 6, 13, 27, 64 0

All (6) RSRZ outliers are listed below:

Mol Chain Res Type RSRZ1 A 22 GLU 4.41 A 20 GLY 4.11 A 19 ALA 2.91 A 23 ALA 2.41 A 21 ALA 2.21 A 128 THR 2.1

6.2 Non-standard residues in protein, DNA, RNA chains iO

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

6.3 Carbohydrates iO

There are no monosaccharides in this entry.

6.4 Ligands iO

In the following table, the Atoms column lists the number of modelled atoms in the group and thenumber de�ned 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<0.92 ATP A 401 31/31 0.97 0.08 3,7,16,21 0

Continued on next page...

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Continued from previous page...

Mol Type Chain Res Atoms RSCC RSR B-factors(Å2) Q<0.93 MN A 404 1/1 0.99 0.23 27,27,27,27 03 MN A 403 1/1 0.99 0.14 20,20,20,20 03 MN A 402 1/1 1.00 0.04 7,7,7,7 0

The following is a graphical depiction of the model �t 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 �t is shown from di�erentorientation to approximate a three-dimensional view.

Electron density around ATP A 401:

2mFo-DFc (at 0.7 rmsd) in gray

mFo-DFc (at 3 rmsd) in purple (negative)

and green (positive)

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Electron density around MN A 404:

2mFo-DFc (at 0.7 rmsd) in gray

mFo-DFc (at 3 rmsd) in purple (negative)

and green (positive)

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Electron density around MN A 403:

2mFo-DFc (at 0.7 rmsd) in gray

mFo-DFc (at 3 rmsd) in purple (negative)

and green (positive)

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Electron density around MN A 402:

2mFo-DFc (at 0.7 rmsd) in gray

mFo-DFc (at 3 rmsd) in purple (negative)

and green (positive)

6.5 Other polymers iO

There are no such residues in this entry.