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i Full wwPDB X-ray Structure Validation Report ○ Feb 12, 2017 – 11:32 pm GMT PDB ID Title Authors Deposited on Resolution : : : : : 4WN0 Xenopus laevis embryonic epidermal lectin in complex with glycerol phosphate Wangkanont, K.; Kiessling, L.L.; Forest, K.T. 2014-10-10 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 [email protected] A user guide is available at http://wwpdb.org/validation/2016/XrayValidationReportHelp i symbol. with specific help available everywhere you see the ○ i were used in the production of this report: The following versions of software and data (see references ○) MolProbity Mogul Xtriage (Phenix) EDS Percentile statistics Refmac CCP4 Ideal geometry (proteins) Ideal geometry (DNA, RNA) Validation Pipeline (wwPDB-VP) : : : : : : : : : : 4.02b-467 1.7.2 (RC1), CSD as538be (2017) 1.9-1692 trunk28620 20161228.v01 (using entries in the PDB archive December 28th 2016) 5.8.0135 6.5.0 Engh & Huber (2001) Parkinson et al. (1996) recalc28949 Page 2 1 Full wwPDB X-ray Structure Validation Report 4WN0 i Overall quality at a glance ○ 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 in the following graphic. The table shows the number of entries on which the scores are based. Metric Rf ree Clashscore Ramachandran outliers Sidechain outliers RSRZ outliers Whole archive (#Entries) 100719 112137 110173 110143 101464 Similar resolution (#Entries, resolution range(Å)) 4002 (2.20-2.20) 4730 (2.20-2.20) 4656 (2.20-2.20) 4657 (2.20-2.20) 4033 (2.20-2.20) The table below summarises the geometric issues observed across the polymeric chains and their fit to the electron density. The red, orange, yellow and green segments on the lower bar indicate the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. 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 dot representing fractions <=5% The upper red bar (where present) indicates the fraction of residues that have poor fit to the electron density. The numeric value is given above the bar. Mol Chain Length 1 A 289 Quality of chain The following table lists non-polymeric compounds, carbohydrate monomers and non-standard residues in protein, DNA, RNA chains that are outliers for geometric or electron-density-fit criteria: Mol 4 4 Type 1PE 1PE Chain A A Res 405 406 Chirality - Geometry - Clashes Electron density X X Continued on next page... Page 3 Full wwPDB X-ray Structure Validation Report Continued from previous page... Mol Type Chain Res Chirality 4 1PE A 407 4 1PE A 408 - Geometry - Clashes - Electron density X X 4WN0 Page 4 2 Full wwPDB X-ray Structure Validation Report 4WN0 i Entry composition ○ There are 6 unique types of molecules in this entry. The entry contains 2400 atoms, of which 0 are hydrogens and 0 are deuteriums. In the tables below, the ZeroOcc column contains the number of atoms modelled with zero occupancy, the AltConf column contains the number of residues with at least one atom in alternate conformation and the Trace column contains the number of residues modelled with at most 2 atoms. • Molecule 1 is a protein called XEEL protein. Mol Chain Residues 1 A 277 Atoms Total C N 2151 1348 367 O 422 S 14 ZeroOcc AltConf Trace 0 2 0 • Molecule 2 is CALCIUM ION (three-letter code: CA) (formula: Ca). Mol Chain Residues 2 A 3 Atoms Total Ca 3 3 ZeroOcc AltConf 0 0 • Molecule 3 is PHOSPHATE ION (three-letter code: PO4) (formula: O4 P). Mol Chain Residues 3 A 1 Atoms Total O P 5 4 1 ZeroOcc AltConf 0 0 • Molecule 4 is PENTAETHYLENE GLYCOL (three-letter code: 1PE) (formula: C10 H22 O6 ). Page 5 Full wwPDB X-ray Structure Validation Report Mol Chain Residues 4 A 1 4 A 1 4 A 1 4 A 1 Atoms Total C 16 10 Total C 16 10 Total C 16 10 Total C 16 10 O 6 O 6 O 6 O 6 ZeroOcc AltConf 0 0 0 0 0 0 0 0 4WN0 • Molecule 5 is S N - G L Y C E R O L - 3 - P H O S P H A T E (three-letter code: G3P) (formula: C3 H9 O6 P). Page 6 Full wwPDB X-ray Structure Validation Report Mol Chain Residues 5 A 1 Atoms Total C O 10 3 6 P 1 ZeroOcc AltConf 0 0 • Molecule 6 is water. Mol Chain Residues 6 A 167 Atoms Total O 167 167 ZeroOcc AltConf 0 0 4WN0 Page 7 3 Full wwPDB X-ray Structure Validation Report 4WN0 i Residue-property plots ○ These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic for a 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 geometry and electron density. Residues are color-coded according to the number of geometric quality criteria for 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 2 or more consecutive residues without any outlier are shown as a green connector. Residues present in the sample, but not in the model, are shown in grey. • Molecule 1: XEEL protein F340 Y341 R342 L315 S305 P306 • K286 L279 S272 T261 L251 K247 G243 K222 W190 M187 A177 W108 D100 ARG SER GLY GLY SER PRO THR GLY ASP MET ASN TYR G66 • Chain A: Page 8 4 Full wwPDB X-ray Structure Validation Report 4WN0 i Data and refinement statistics ○ Property Space group Cell constants a, b, c, α, β, γ Resolution (Å) % Data completeness (in resolution range) Rmerge Rsym < I/σ(I) > 1 Refinement program R, Rf ree Rf ree test set Wilson B-factor (Å2 ) Anisotropy Bulk solvent ksol (e/Å3 ), Bsol (Å2 ) L-test for twinning2 Estimated twinning fraction Fo ,Fc correlation Total number of atoms Average B, all atoms (Å2 ) Value P6 124.63Å 124.63Å 55.59Å 90.00◦ 90.00◦ 120.00◦ 29.93 – 2.20 30.20 – 2.20 99.8 (29.93-2.20) 96.7 (30.20-2.20) (Not available) 0.13 3.47 (at 2.20Å) PHENIX 0.151 , 0.169 0.144 , 0.167 1258 reflections (4.99%) 29.6 0.267 0.40 , 54.9 < |L| > = 0.49, < L2 > = 0.32 0.043 for h,-h-k,-l 0.97 2400 25.0 Source Depositor Depositor Depositor EDS Depositor EDS Depositor Depositor Xtriage Depositor Depositor DCC DCC Xtriage Xtriage EDS Xtriage Xtriage EDS wwPDB-VP wwPDB-VP Xtriage’s analysis on translational NCS is as follows: The largest off-origin peak in the Patterson function is 5.12% of the height of the origin peak. No significant pseudotranslation is detected. Intensities estimated from amplitudes. Theoretical 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. 1 2 Page 9 5 Full wwPDB X-ray Structure Validation Report 4WN0 i Model quality ○ 5.1 i Standard geometry ○ Bond lengths and bond angles in the following residue types are not validated in this section: G3P, CA, PO4, 1PE The Z score for a bond length (or angle) is the number of standard deviations the observed value is removed from the expected value. A bond length (or angle) with |Z| > 5 is considered an outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles). Mol Chain 1 A Bond lengths RMSZ #|Z| >5 0.37 0/2207 Bond angles RMSZ #|Z| >5 0.54 0/2994 There are no bond length outliers. There are no bond angle outliers. There are no chirality outliers. There are no planarity outliers. 5.2 i Too-close contacts ○ In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms and hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogen atoms added and optimized by MolProbity. The Clashes column lists the number of clashes within the asymmetric unit, whereas Symm-Clashes lists symmetry related clashes. Mol 1 2 3 4 5 6 All Chain A A A A A A All Non-H 2151 3 5 64 10 167 2400 H(model) 0 0 0 0 0 0 0 H(added) 2007 0 0 88 5 0 2100 Clashes 10 0 1 7 0 1 12 Symm-Clashes 0 0 0 0 0 0 0 The all-atom clashscore is defined as the number of clashes found per 1000 atoms (including hydrogen atoms). The all-atom clashscore for this structure is 3. All (12) close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude. Page 10 Full wwPDB X-ray Structure Validation Report Atom-1 Atom-2 3:A:404:PO4:O2 1:A:243:GLY:H 1:A:286:LYS:HD3 1:A:100:ASP:HB3 1:A:261:THR:OG1 4:A:408:1PE:H141 1:A:222:LYS:HD2 1:A:187:MET:HA 1:A:247:LYS:HZ1 1:A:305:SER:HA 1:A:306:PRO:HD2 1:A:177:ALA:HB3 6:A:630:HOH:O 4:A:407:1PE:H152 4:A:406:1PE:H141 1:A:108:TRP:HB2 4:A:406:1PE:H231 4:A:408:1PE:H162 4:A:405:1PE:H242 1:A:190:TRP:CE2 4:A:407:1PE:H222 1:A:306:PRO:HA 4:A:408:1PE:H261 1:A:340:PHE:HB2 Interatomic distance (Å) 2.18 1.73 1.92 1.92 2.12 1.95 1.97 2.55 1.84 1.78 2.01 2.04 4WN0 Clash overlap (Å) 0.57 0.53 0.52 0.51 0.49 0.49 0.46 0.42 0.42 0.41 0.41 0.40 There are no symmetry-related clashes. 5.3 5.3.1 i Torsion angles ○ i Protein backbone ○ In the following table, the Percentiles column shows the percent Ramachandran outliers of the chain as a percentile score with respect to all X-ray entries followed by that with respect to entries of similar resolution. The Analysed column shows the number of residues for which the backbone conformation was analysed, and the total number of residues. Mol Chain Analysed Favoured Allowed Outliers 1 A 277/289 (96%) 265 (96%) 12 (4%) 0 Percentiles 100 100 There are no Ramachandran outliers to report. 5.3.2 i Protein sidechains ○ In the following table, the Percentiles column shows the percent sidechain outliers of the chain as a percentile score with respect to all X-ray entries followed by that with respect to entries of similar resolution. The Analysed column shows the number of residues for which the sidechain conformation was analysed, and the total number of residues. Page 11 Full wwPDB X-ray Structure Validation Report Mol Chain Analysed Rotameric Outliers 1 A 225/232 (97%) 222 (99%) 3 (1%) 4WN0 Percentiles 73 85 All (3) residues with a non-rotameric sidechain are listed below: Mol 1 1 1 Chain A A A Res 251 272 315 Type LEU SER LEU Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. There are no such sidechains identified. 5.3.3 i RNA ○ There are no RNA molecules in this entry. 5.4 i Non-standard residues in protein, DNA, RNA chains ○ There are no non-standard protein/DNA/RNA residues in this entry. 5.5 i Carbohydrates ○ There are no carbohydrates in this entry. 5.6 i Ligand geometry ○ Of 9 ligands modelled in this entry, 3 are monoatomic - leaving 6 for Mogul analysis. In the following table, the Counts columns list the number of bonds (or angles) for which Mogul statistics could be retrieved, the number of bonds (or angles) that are observed in the model and the number of bonds (or angles) that are defined in the chemical component dictionary. The Link column lists molecule types, if any, to which the group is linked. The Z score for a bond length (or angle) is the number of standard deviations the observed value is removed from the expected 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 3 4 4 PO4 1PE 1PE A A A 404 405 406 - Bond lengths Counts RMSZ #|Z| > 2 4,4,4 0.77 0 15,15,15 0.62 0 15,15,15 0.59 0 Bond angles Counts RMSZ #|Z| > 2 6,6,6 0.39 0 14,14,14 0.84 0 14,14,14 0.89 0 Page 12 Full wwPDB X-ray Structure Validation Report Mol Type Chain Res Link 4 4 5 1PE 1PE G3P A A A 407 408 409 2 Bond lengths Counts RMSZ #|Z| > 2 15,15,15 0.62 0 15,15,15 0.65 0 9,9,9 1.55 2 (22%) 4WN0 Bond angles Counts RMSZ #|Z| > 2 14,14,14 0.92 0 14,14,14 0.77 0 11,12,12 1.18 1 (9%) In the following table, the Chirals column lists the number of chiral outliers, the number of chiral centers analysed, the number of these observed in the model and the number defined in the chemical component dictionary. Similar counts are reported in the Torsion and Rings columns. ’-’ means no outliers of that kind were identified. Mol 3 4 4 4 4 5 Type PO4 1PE 1PE 1PE 1PE G3P Chain A A A A A A Res 404 405 406 407 408 409 Link 2 Chirals - Torsions 0/0/0/0 0/13/13/13 0/13/13/13 0/13/13/13 0/13/13/13 0/8/8/8 Rings 0/0/0/0 0/0/0/0 0/0/0/0 0/0/0/0 0/0/0/0 0/0/0/0 All (2) bond length outliers are listed below: Mol 5 5 Chain A A Res 409 409 Type G3P G3P Atoms P-O4P P-O2P Z 2.00 3.75 Observed(Å) 1.63 1.63 Ideal(Å) 1.54 1.50 All (1) bond angle outliers are listed below: Mol 5 Chain A Res 409 Type G3P Atoms O3P-P-O1P Z 2.81 Observed(o ) 114.21 There are no chirality outliers. There are no torsion outliers. There are no ring outliers. 5 monomers are involved in 8 short contacts: Mol 3 4 4 4 4 Chain A A A A A Res 404 405 406 407 408 Type PO4 1PE 1PE 1PE 1PE Clashes 1 1 2 2 2 Symm-Clashes 0 0 0 0 0 Ideal(o ) 106.73 Page 13 5.7 Full wwPDB X-ray Structure Validation Report i Other polymers ○ There are no such residues in this entry. 5.8 i Polymer linkage issues ○ There are no chain breaks in this entry. 4WN0 Page 14 6 Full wwPDB X-ray Structure Validation Report 4WN0 i Fit of model and data ○ 6.1 i Protein, DNA and RNA chains ○ 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 to all 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 per residue. The column labelled ‘Q< 0.9’ lists the number of (and percentage) of residues with an average occupancy less than 0.9. Mol Chain Analysed <RSRZ> 1 A 277/289 (95%) -0.55 #RSRZ>2 2 (0%) 87 86 OWAB(Å2 ) Q<0.9 15, 23, 34, 51 0 All (2) RSRZ outliers are listed below: Mol 1 1 6.2 Chain A A Res 66 279 Type GLY LEU RSRZ 3.8 2.1 i Non-standard residues in protein, DNA, RNA chains ○ There are no non-standard protein/DNA/RNA residues in this entry. 6.3 i Carbohydrates ○ There are no carbohydrates in this entry. 6.4 i Ligands ○ In the following table, the Atoms column lists the number of modelled atoms in the group and the number defined in the chemical component dictionary. LLDF column lists the quality of electron density of the group with respect to its neighbouring residues in protein, DNA or RNA chains. The B-factors column lists the minimum, median, 95th percentile and maximum values of B factors of atoms in the group. The column labelled ‘Q< 0.9’ lists the number of atoms with occupancy less than 0.9. Mol 4 4 4 Type 1PE 1PE 1PE Chain A A A Res 408 407 405 Atoms 16/16 16/16 16/16 RSCC 0.84 0.79 0.84 RSR 0.42 0.38 0.26 LLDF 30.08 13.13 9.65 B-factors(Å2 ) Q<0.9 45,51,65,67 0 44,51,62,63 0 47,53,61,66 0 Continued on next page... Page 15 Full wwPDB X-ray Structure Validation Report Continued from previous page... Mol Type Chain Res Atoms 4 1PE A 406 16/16 5 G3P A 409 10/10 2 CA A 402 1/1 2 CA A 401 1/1 2 CA A 403 1/1 3 PO4 A 404 5/5 6.5 i Other polymers ○ There are no such residues in this entry. RSCC 0.72 0.84 0.99 0.99 0.99 0.79 RSR 0.28 0.14 0.07 0.04 0.03 0.35 LLDF 2.98 0.92 -1.19 -2.18 -3.80 - B-factors(Å2 ) 46,52,63,64 21,30,52,65 15,15,15,15 15,15,15,15 20,20,20,20 61,67,82,83 4WN0 Q<0.9 0 0 0 0 0 0