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Full wwPDB EM Validation Report i○
Dec 15, 2020 – 12:19 PM JST
PDB ID : 5Z10EMDB ID : EMD-6865
Title : Structure of the mechanosensitive Piezo1 channelAuthors : Zhao, Q.; Zhou, H.; Chi, S.; Wang, Y.; Wang, J.; Geng, J.; Wu, K.; Liu, W.;
Zhang, T.; Dong, M.-Q.; Wang, J.; Li, X.; Xiao, B.Deposited on : 2017-12-22
Resolution : 3.97 Å(reported)
This is a Full wwPDB EM 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/EMValidationReportHelpwith 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:
EMDB validation analysis : 0.0.0.dev61MolProbity : 4.02b-467
Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)Ideal geometry (proteins) : Engh & Huber (2001)
Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : 2.15.1
https://www.wwpdb.org/validation/2017/EMValidationReportHelphttps://www.wwpdb.org/validation/2017/EMValidationReportHelphttps://www.wwpdb.org/validation/2017/EMValidationReportHelphttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#references
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Page 2 Full wwPDB EM Validation Report EMD-6865, 5Z10
1 Overall quality at a glance i○
The following experimental techniques were used to determine the structure:ELECTRON MICROSCOPY
The reported resolution of this entry is 3.97 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)EM structures(#Entries)
Clashscore 158937 4297Ramachandran outliers 154571 4023
Sidechain outliers 154315 3826
The table below summarises the geometric issues observed across the polymeric chains and their fitto the map. The red, orange, yellow and green segments of the bar indicate the fraction of residuesthat contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. A greysegment 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
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Page 3 Full wwPDB EM Validation Report EMD-6865, 5Z10
2 Entry composition i○
There is only 1 type of molecule in this entry. The entry contains 29142 atoms, of which 0 arehydrogens and 0 are deuteriums.
In the tables below, the AltConf column contains the number of residues with at least one atomin alternate conformation and the Trace column contains the number of residues modelled with atmost 2 atoms.
• Molecule 1 is a protein called Piezo-type mechanosensitive ion channel component 1.
Mol Chain Residues Atoms AltConf Trace
1 A 1304 Total C N O S9714 6308 1666 1701 39 0 0
1 B 1304 Total C N O S9714 6308 1666 1701 39 0 0
1 C 1304 Total C N O S9714 6308 1666 1701 39 0 0
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#entry_composition
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Page 4 Full wwPDB EM Validation Report EMD-6865, 5Z10
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 andatom inclusion in map density. Residues are color-coded according to the number of geometricquality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2and red = 3 or more. A red diamond above a residue indicates a poor fit to the EM map forthis residue (all-atom inclusion < 40%). Stretches of 2 or more consecutive residues without anyoutlier are shown as a green connector. Residues present in the sample, but not in the model, areshown in grey.
• Molecule 1: Piezo-type mechanosensitive ion channel component 1
Chain A:
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Page 5 Full wwPDB EM Validation Report EMD-6865, 5Z10
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Page 6 Full wwPDB EM Validation Report EMD-6865, 5Z10
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• Molecule 1: Piezo-type mechanosensitive ion channel component 1
Chain B:
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Page 7 Full wwPDB EM Validation Report EMD-6865, 5Z10
P841
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-
Page 8 Full wwPDB EM Validation Report EMD-6865, 5Z10
D239
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• Molecule 1: Piezo-type mechanosensitive ion channel component 1
Chain C:
MET
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PRO
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VAL
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Page 9 Full wwPDB EM Validation Report EMD-6865, 5Z10
T111
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Page 10 Full wwPDB EM Validation Report EMD-6865, 5Z10
4 Experimental information i○
Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C3 DepositorNumber of particles used 238529 DepositorResolution determination method FSC 0.143 CUT-OFF DepositorCTF correction method PHASE FLIPPING AND AMPLITUDE
CORRECTIONDepositor
Microscope FEI TITAN KRIOS DepositorVoltage (kV) 300 DepositorElectron dose (e−/Å2) 50 DepositorMinimum defocus (nm) 3000 DepositorMaximum defocus (nm) Not providedMagnification 22500 DepositorImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 0.300 DepositorMinimum map value -0.193 DepositorAverage map value 0.001 DepositorMap value standard deviation 0.006 DepositorRecommended contour level 0.027 DepositorMap size (Å) 369.6, 369.6, 369.6 wwPDBMap dimensions 280, 280, 280 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.32, 1.32, 1.32 Depositor
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#experimental_info
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Page 11 Full wwPDB EM Validation Report EMD-6865, 5Z10
5 Model quality i○
5.1 Standard geometry i○
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| >51 A 0.36 0/9920 0.59 3/13499 (0.0%)1 B 0.36 0/9920 0.59 3/13499 (0.0%)1 C 0.36 0/9920 0.59 3/13499 (0.0%)All All 0.36 0/29760 0.59 9/40497 (0.0%)
Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifying ifthe center is modelled as a planar moiety or with the opposite hand.A planarity outlier is detectedby checking planarity of atoms in a peptide group, atoms in a mainchain group or atoms of asidechain that are expected to be planar.
Mol Chain #Chirality outliers #Planarity outliers1 A 0 21 B 0 21 C 0 2All All 0 6
There are no bond length outliers.
All (9) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 A 1987 ASP CB-CG-OD1 7.41 124.97 118.301 C 1987 ASP CB-CG-OD1 7.38 124.94 118.301 B 1987 ASP CB-CG-OD1 7.37 124.94 118.301 A 2434 LEU CA-CB-CG 6.45 130.13 115.301 B 2434 LEU CA-CB-CG 6.45 130.13 115.301 C 2434 LEU CA-CB-CG 6.43 130.08 115.301 A 1801 LEU CA-CB-CG 5.80 128.65 115.301 B 1801 LEU CA-CB-CG 5.80 128.65 115.301 C 1801 LEU CA-CB-CG 5.80 128.63 115.30
There are no chirality outliers.
All (6) planarity outliers are listed below:
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#model_qualityhttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#standard_geometry
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Page 12 Full wwPDB EM Validation Report EMD-6865, 5Z10
Mol Chain Res Type Group1 A 1724 ARG Peptide1 A 1975 ASP Peptide1 B 1724 ARG Peptide1 B 1975 ASP Peptide1 C 1724 ARG Peptide1 C 1975 ASP Peptide
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 9714 0 8963 124 01 B 9714 0 8963 124 01 C 9714 0 8963 127 0All All 29142 0 26889 357 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 6.
All (357) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)1:A:2406:ARG:O 1:A:2428:GLU:HA 1.74 0.881:B:2406:ARG:O 1:B:2428:GLU:HA 1.74 0.871:C:2406:ARG:O 1:C:2428:GLU:HA 1.74 0.86
1:A:2035:ARG:HH21 1:A:2039:LEU:HD11 1.52 0.741:B:2035:ARG:HH21 1:B:2039:LEU:HD11 1.52 0.731:C:2035:ARG:HH21 1:C:2039:LEU:HD11 1.52 0.721:A:1695:ILE:HG21 1:A:1714:VAL:HG21 1.75 0.681:B:1695:ILE:HG21 1:B:1714:VAL:HG21 1.75 0.671:C:1695:ILE:HG21 1:C:1714:VAL:HG21 1.75 0.671:C:1140:ILE:HA 1:C:1143:PHE:HB2 1.78 0.661:B:1140:ILE:HA 1:B:1143:PHE:HB2 1.78 0.651:C:2376:ILE:HA 1:C:2386:PRO:HA 1.80 0.641:A:2376:ILE:HA 1:A:2386:PRO:HA 1.80 0.641:A:1140:ILE:HA 1:A:1143:PHE:HB2 1.78 0.641:B:1338:GLU:O 1:B:2104:ARG:NH1 2.31 0.64
Continued on next page...
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#close_contacts
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Page 13 Full wwPDB EM Validation Report EMD-6865, 5Z10
Continued from previous page...
Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)1:C:1338:GLU:O 1:C:2104:ARG:NH1 2.31 0.641:B:2376:ILE:HA 1:B:2386:PRO:HA 1.80 0.631:A:2376:ILE:HB 1:A:2448:ILE:HG22 1.81 0.631:A:1338:GLU:O 1:A:2104:ARG:NH1 2.31 0.63
1:C:2404:GLN:HB2 1:C:2431:VAL:HB 1.82 0.621:B:2376:ILE:HB 1:B:2448:ILE:HG22 1.80 0.621:B:2404:GLN:HB2 1:B:2431:VAL:HB 1.81 0.611:C:2376:ILE:HB 1:C:2448:ILE:HG22 1.80 0.611:C:1987:ASP:OD1 1:C:2082:TRP:NE1 2.33 0.611:A:2404:GLN:HB2 1:A:2431:VAL:HB 1.81 0.611:B:2380:ASN:ND2 1:B:2452:LYS:O 2.34 0.611:A:1987:ASP:OD1 1:A:2082:TRP:NE1 2.33 0.601:B:1987:ASP:OD1 1:B:2082:TRP:NE1 2.33 0.601:C:1984:ASP:OD1 1:C:2027:GLN:NE2 2.34 0.601:A:1984:ASP:OD1 1:A:2027:GLN:NE2 2.34 0.601:B:1984:ASP:OD1 1:B:2027:GLN:NE2 2.34 0.601:A:2380:ASN:ND2 1:A:2452:LYS:O 2.34 0.601:A:1155:VAL:HA 1:A:1158:PHE:HB2 1.84 0.591:C:2380:ASN:ND2 1:C:2452:LYS:O 2.34 0.591:A:2387:VAL:HG12 1:A:2389:GLN:H 1.68 0.591:C:2387:VAL:HG12 1:C:2389:GLN:H 1.67 0.591:B:1155:VAL:HA 1:B:1158:PHE:HB2 1.84 0.591:C:1155:VAL:HA 1:C:1158:PHE:HB2 1.84 0.59
1:B:1024:ARG:HH12 1:B:1294:ARG:HE 1.52 0.581:A:1146:CYS:HB2 1:A:1662:ALA:HB2 1.86 0.581:B:2387:VAL:HG12 1:B:2389:GLN:H 1.67 0.581:A:1024:ARG:HH12 1:A:1294:ARG:HE 1.52 0.581:B:2169:ARG:NH2 1:B:2497:LEU:O 2.35 0.581:C:1024:ARG:HH12 1:C:1294:ARG:HE 1.52 0.581:A:2169:ARG:NH2 1:A:2497:LEU:O 2.35 0.571:C:2169:ARG:NH2 1:C:2497:LEU:O 2.35 0.571:A:2108:ASN:OD1 1:A:2135:ARG:NH2 2.38 0.571:C:1146:CYS:HB2 1:C:1662:ALA:HB2 1.86 0.571:B:2108:ASN:OD1 1:B:2135:ARG:NH2 2.38 0.571:A:2375:TYR:HA 1:A:2447:VAL:O 2.05 0.561:B:1146:CYS:HB2 1:B:1662:ALA:HB2 1.86 0.561:C:2108:ASN:OD1 1:C:2135:ARG:NH2 2.38 0.561:A:1188:CYS:O 1:A:1192:LEU:HB2 2.06 0.56
1:A:1344:GLN:OE1 1:A:1347:ARG:NH1 2.39 0.561:A:1559:LEU:HA 1:A:1654:LEU:HD13 1.88 0.561:A:1687:SER:O 1:A:1796:HIS:ND1 2.38 0.56
Continued on next page...
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Page 14 Full wwPDB EM Validation Report EMD-6865, 5Z10
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Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)1:B:2347:ASN:OD1 1:B:2352:ARG:NH2 2.39 0.561:B:2535:SER:OG 1:B:2538:THR:OG1 2.23 0.561:C:2375:TYR:HA 1:C:2447:VAL:O 2.05 0.561:B:1559:LEU:HA 1:B:1654:LEU:HD13 1.88 0.561:B:1194:PHE:HB3 1:B:1198:LEU:HD23 1.88 0.561:C:2347:ASN:OD1 1:C:2352:ARG:NH2 2.39 0.551:B:2375:TYR:HA 1:B:2447:VAL:O 2.05 0.551:A:1194:PHE:HB3 1:A:1198:LEU:HD23 1.88 0.551:A:1711:PRO:HA 1:A:1714:VAL:HB 1.89 0.551:C:1194:PHE:HB3 1:C:1198:LEU:HD23 1.88 0.551:C:2245:GLN:HG2 1:C:2246:PRO:HD3 1.88 0.551:A:2245:GLN:HG2 1:A:2246:PRO:HD3 1.88 0.551:C:1188:CYS:O 1:C:1192:LEU:HB2 2.06 0.551:C:1201:LYS:O 1:C:1206:GLN:NE2 2.40 0.55
1:A:2347:ASN:OD1 1:A:2352:ARG:NH2 2.39 0.551:B:1188:CYS:O 1:B:1192:LEU:HB2 2.06 0.55
1:B:1344:GLN:OE1 1:B:1347:ARG:NH1 2.39 0.551:C:1344:GLN:OE1 1:C:1347:ARG:NH1 2.39 0.551:A:1201:LYS:O 1:A:1206:GLN:NE2 2.40 0.551:B:1711:PRO:HA 1:B:1714:VAL:HB 1.89 0.551:B:1201:LYS:O 1:B:1206:GLN:NE2 2.40 0.54
1:C:1711:PRO:HA 1:C:1714:VAL:HB 1.89 0.541:A:2377:ARG:HA 1:A:2449:PHE:HB2 1.90 0.541:B:2245:GLN:HG2 1:B:2246:PRO:HD3 1.88 0.541:C:2377:ARG:HA 1:C:2449:PHE:HB2 1.90 0.541:B:703:GLN:O 1:B:708:HIS:N 2.40 0.54
1:A:2535:SER:OG 1:A:2538:THR:OG1 2.23 0.541:A:703:GLN:O 1:A:708:HIS:N 2.40 0.54
1:C:1559:LEU:HA 1:C:1654:LEU:HD13 1.88 0.541:A:2283:THR:HG23 1:A:2447:VAL:HG22 1.90 0.54
1:C:1687:SER:O 1:C:1796:HIS:ND1 2.38 0.541:C:2148:SER:OG 1:C:2149:LEU:N 2.41 0.541:A:1168:VAL:HA 1:A:1171:VAL:HG12 1.90 0.541:A:2148:SER:OG 1:A:2149:LEU:N 2.41 0.541:C:703:GLN:O 1:C:708:HIS:N 2.40 0.53
1:B:2377:ARG:HA 1:B:2449:PHE:HB2 1.90 0.531:B:2365:SER:HB3 1:B:2402:ARG:HD3 1.90 0.531:C:1168:VAL:HA 1:C:1171:VAL:HG12 1.90 0.531:A:2496:GLU:O 1:B:2534:ARG:NH1 2.42 0.531:B:1687:SER:O 1:B:1796:HIS:ND1 2.38 0.531:B:2545:GLU:O 1:B:2546:ARG:NH2 2.42 0.53
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Page 15 Full wwPDB EM Validation Report EMD-6865, 5Z10
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Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)1:B:2496:GLU:O 1:C:2534:ARG:NH1 2.42 0.53
1:C:2365:SER:HB3 1:C:2402:ARG:HD3 1.90 0.531:B:1716:LEU:HD11 1:B:2051:VAL:HG12 1.91 0.531:A:2534:ARG:NH1 1:C:2496:GLU:O 2.41 0.521:B:2148:SER:OG 1:B:2149:LEU:N 2.41 0.521:A:2356:GLN:HG3 1:A:2364:GLN:HG2 1.92 0.521:A:2545:GLU:O 1:A:2546:ARG:NH2 2.42 0.52
1:B:2356:GLN:HG3 1:B:2364:GLN:HG2 1.92 0.521:B:2283:THR:HG23 1:B:2447:VAL:HG22 1.90 0.521:C:2252:THR:HG23 1:C:2255:ALA:H 1.75 0.521:A:2365:SER:HB3 1:A:2402:ARG:HD3 1.90 0.521:C:2283:THR:HG23 1:C:2447:VAL:HG22 1.90 0.521:A:1403:HIS:ND1 1:A:1403:HIS:O 2.43 0.521:B:1403:HIS:ND1 1:B:1403:HIS:O 2.43 0.52
1:B:2252:THR:HG23 1:B:2255:ALA:H 1.75 0.521:C:2535:SER:OG 1:C:2538:THR:OG1 2.23 0.521:B:1168:VAL:HA 1:B:1171:VAL:HG12 1.90 0.521:C:1403:HIS:O 1:C:1403:HIS:ND1 2.43 0.521:C:2545:GLU:O 1:C:2546:ARG:NH2 2.42 0.521:A:2110:LEU:O 1:A:2118:ASN:ND2 2.42 0.52
1:B:2409:GLN:NE2 1:B:2425:ASP:OD2 2.43 0.511:C:1716:LEU:HD11 1:C:2051:VAL:HG12 1.91 0.511:A:2409:GLN:NE2 1:A:2425:ASP:OD2 2.43 0.511:C:2356:GLN:HG3 1:C:2364:GLN:HG2 1.91 0.511:C:2409:GLN:NE2 1:C:2425:ASP:OD2 2.43 0.511:A:2252:THR:HG23 1:A:2255:ALA:H 1.75 0.511:B:2220:VAL:HA 1:B:2452:LYS:HG3 1.93 0.50
1:A:1716:LEU:HD11 1:A:2051:VAL:HG12 1.91 0.501:A:2519:LEU:HD13 1:C:2183:LYS:HD3 1.93 0.501:C:2220:VAL:HA 1:C:2452:LYS:HG3 1.93 0.50
1:C:2513:VAL:HG11 1:C:2521:LEU:HB3 1.94 0.501:A:2471:VAL:HA 1:A:2474:VAL:HG12 1.93 0.501:B:2183:LYS:HD3 1:C:2519:LEU:HD13 1.94 0.501:B:2368:ILE:HG13 1:B:2401:VAL:HB 1.94 0.501:B:988:LYS:HD3 1:B:1026:ARG:HH12 1.77 0.501:C:1196:THR:O 1:C:1200:GLN:NE2 2.45 0.501:C:2372:PHE:O 1:C:2399:LEU:N 2.45 0.501:C:2471:VAL:HA 1:C:2474:VAL:HG12 1.93 0.501:A:2231:LYS:HA 1:A:2237:PRO:HA 1.94 0.501:B:2345:ALA:HB3 1:B:2348:SER:HB3 1.94 0.491:A:988:LYS:HD3 1:A:1026:ARG:HH12 1.77 0.49
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Page 16 Full wwPDB EM Validation Report EMD-6865, 5Z10
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Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)1:B:2513:VAL:HG11 1:B:2521:LEU:HB3 1.94 0.491:A:1196:THR:O 1:A:1200:GLN:NE2 2.45 0.49
1:A:1159:ARG:NH2 1:A:1308:ASP:OD2 2.46 0.491:C:1159:ARG:NH2 1:C:1308:ASP:OD2 2.46 0.491:C:988:LYS:HD3 1:C:1026:ARG:HH12 1.77 0.491:A:2372:PHE:O 1:A:2399:LEU:N 2.45 0.49
1:A:2513:VAL:HG11 1:A:2521:LEU:HB3 1.94 0.491:A:2534:ARG:HH12 1:C:2498:PRO:HD3 1.78 0.491:B:1196:THR:O 1:B:1200:GLN:NE2 2.45 0.49
1:B:1159:ARG:NH2 1:B:1308:ASP:OD2 2.46 0.491:B:2110:LEU:O 1:B:2118:ASN:ND2 2.42 0.491:A:2220:VAL:HA 1:A:2452:LYS:HG3 1.93 0.49
1:B:2221:ASN:HD21 1:B:2325:ARG:HB2 1.78 0.491:C:2368:ILE:HG13 1:C:2401:VAL:HB 1.94 0.491:A:2368:ILE:HG13 1:A:2401:VAL:HB 1.94 0.491:A:2268:LEU:HB3 1:A:2389:GLN:HG3 1.95 0.491:B:2231:LYS:HA 1:B:2237:PRO:HA 1.94 0.481:B:2268:LEU:HB3 1:B:2389:GLN:HG3 1.95 0.481:A:2338:GLU:OE1 1:A:2385:ASN:ND2 2.46 0.481:B:2372:PHE:O 1:B:2399:LEU:N 2.45 0.481:B:2471:VAL:HA 1:B:2474:VAL:HG12 1.93 0.481:C:2345:ALA:HB3 1:C:2348:SER:HB3 1.94 0.481:C:2221:ASN:HD21 1:C:2325:ARG:HB2 1.78 0.481:A:2221:ASN:HD21 1:A:2325:ARG:HB2 1.78 0.481:C:2231:LYS:HA 1:C:2237:PRO:HA 1.94 0.481:A:1403:HIS:NE2 1:A:2146:THR:O 2.40 0.481:A:2345:ALA:HB3 1:A:2348:SER:HB3 1.94 0.481:B:2338:GLU:OE1 1:B:2385:ASN:ND2 2.46 0.481:A:2183:LYS:HD3 1:B:2519:LEU:HD13 1.94 0.481:B:2498:PRO:HD3 1:C:2534:ARG:HH12 1.78 0.481:A:2057:ILE:HG12 1:A:2086:LYS:HD2 1.96 0.471:B:2225:ASP:HB2 1:B:2324:GLN:O 2.14 0.471:C:1651:ASP:OD1 1:C:1651:ASP:N 2.47 0.471:C:2057:ILE:HG12 1:C:2086:LYS:HD2 1.96 0.471:B:2057:ILE:HG12 1:B:2086:LYS:HD2 1.96 0.471:C:2110:LEU:O 1:C:2118:ASN:ND2 2.42 0.47
1:C:2338:GLU:OE1 1:C:2385:ASN:ND2 2.46 0.471:A:2147:LEU:HD23 1:A:2151:ASN:HB3 1.97 0.471:C:2147:LEU:HD23 1:C:2151:ASN:HB3 1.97 0.471:A:1032:LEU:O 1:A:1036:TYR:N 2.48 0.47
1:A:1651:ASP:OD1 1:A:1651:ASP:N 2.47 0.47Continued on next page...
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Page 17 Full wwPDB EM Validation Report EMD-6865, 5Z10
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Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)1:B:2147:LEU:HD23 1:B:2151:ASN:HB3 1.97 0.471:A:2225:ASP:HB2 1:A:2324:GLN:O 2.14 0.471:A:1141:PRO:HD3 1:A:1304:HIS:CG 2.50 0.471:A:1514:ASP:HA 1:A:1517:THR:HG22 1.97 0.471:B:1141:PRO:HD3 1:B:1304:HIS:CG 2.50 0.471:B:2436:ASP:N 1:B:2436:ASP:OD1 2.48 0.471:B:1403:HIS:NE2 1:B:2146:THR:O 2.40 0.461:B:2213:ILE:O 1:B:2457:SER:OG 2.27 0.461:B:1032:LEU:O 1:B:1036:TYR:N 2.48 0.461:C:1403:HIS:NE2 1:C:2146:THR:O 2.40 0.461:C:2184:LYS:HB3 1:C:2187:VAL:HB 1.97 0.461:C:2268:LEU:HB3 1:C:2389:GLN:HG3 1.95 0.461:A:2436:ASP:N 1:A:2436:ASP:OD1 2.48 0.46
1:B:2324:GLN:HG3 1:B:2334:GLU:HG2 1.98 0.461:C:1141:PRO:HD3 1:C:1304:HIS:CG 2.50 0.461:A:2184:LYS:HB3 1:A:2187:VAL:HB 1.97 0.461:C:2225:ASP:HB2 1:C:2324:GLN:O 2.14 0.461:A:2269:ALA:HB1 1:A:2390:LEU:HD13 1.98 0.461:A:2498:PRO:HD3 1:B:2534:ARG:HH12 1.79 0.461:B:1144:ILE:HA 1:B:1155:VAL:HG11 1.98 0.461:B:2493:MET:HA 1:C:2534:ARG:HG3 1.97 0.461:A:2236:GLU:HB2 1:A:2296:ILE:HD13 1.98 0.461:B:2050:GLN:NE2 1:B:2093:SER:OG 2.47 0.461:C:1514:ASP:HA 1:C:1517:THR:HG22 1.97 0.461:B:2269:ALA:HB1 1:B:2390:LEU:HD13 1.98 0.461:A:2324:GLN:HG3 1:A:2334:GLU:HG2 1.98 0.461:A:2420:GLY:O 1:A:2424:SER:N 2.49 0.461:B:967:ARG:NH1 1:B:1116:THR:O 2.49 0.461:B:1514:ASP:HA 1:B:1517:THR:HG22 1.97 0.461:A:2493:MET:HA 1:B:2534:ARG:HG3 1.98 0.461:C:2269:ALA:HB1 1:C:2390:LEU:HD13 1.98 0.461:B:2236:GLU:HB2 1:B:2296:ILE:HD13 1.98 0.451:B:2420:GLY:O 1:B:2424:SER:N 2.49 0.451:C:2535:SER:HG 1:C:2538:THR:HG1 1.55 0.451:A:967:ARG:NH1 1:A:1116:THR:O 2.49 0.451:C:2420:GLY:O 1:C:2424:SER:N 2.49 0.451:C:1032:LEU:O 1:C:1036:TYR:N 2.47 0.451:C:967:ARG:NH1 1:C:1116:THR:O 2.49 0.451:B:1353:ARG:NE 1:B:2518:GLU:OE2 2.41 0.451:A:971:ASP:HA 1:A:1150:LEU:HD11 1.99 0.45
1:C:2221:ASN:OD1 1:C:2325:ARG:NE 2.43 0.45Continued on next page...
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Page 18 Full wwPDB EM Validation Report EMD-6865, 5Z10
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Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)1:C:2324:GLN:HG3 1:C:2334:GLU:HG2 1.98 0.451:A:1144:ILE:HA 1:A:1155:VAL:HG11 1.98 0.451:B:2184:LYS:HB3 1:B:2187:VAL:HB 1.97 0.451:C:2285:GLN:HB3 1:C:2443:LEU:HG 1.99 0.451:A:2534:ARG:HG3 1:C:2493:MET:HA 1.98 0.451:C:971:ASP:HA 1:C:1150:LEU:HD11 1.99 0.45
1:B:1780:ASP:OD1 1:B:1780:ASP:N 2.48 0.441:C:1727:LYS:HG3 1:C:1728:ARG:HG2 1.99 0.441:C:2309:TYR:OH 1:C:2359:GLU:OE2 2.35 0.441:C:2236:GLU:HB2 1:C:2296:ILE:HD13 1.98 0.441:B:1651:ASP:OD1 1:B:1651:ASP:N 2.47 0.441:C:1780:ASP:OD1 1:C:1780:ASP:N 2.48 0.441:C:2538:THR:HG22 1:C:2541:LYS:HE3 2.00 0.441:A:2406:ARG:HD3 1:A:2406:ARG:HA 1.83 0.441:B:1727:LYS:HG3 1:B:1728:ARG:HG2 1.99 0.441:C:2436:ASP:N 1:C:2436:ASP:OD1 2.48 0.441:A:1409:SER:O 1:A:1409:SER:OG 2.36 0.44
1:A:2285:GLN:HB3 1:A:2443:LEU:HG 1.99 0.441:B:2538:THR:HG22 1:B:2541:LYS:HE3 2.00 0.441:C:1144:ILE:HA 1:C:1155:VAL:HG11 1.98 0.441:C:1289:PHE:HD1 1:C:1292:LEU:HD12 1.83 0.441:A:2309:TYR:OH 1:A:2359:GLU:OE2 2.35 0.441:A:2397:ASP:N 1:A:2397:ASP:OD1 2.50 0.44
1:A:2538:THR:HG22 1:A:2541:LYS:HE3 2.00 0.441:C:2050:GLN:NE2 1:C:2093:SER:OG 2.47 0.441:B:593:MET:O 1:B:597:VAL:CB 2.66 0.441:A:1726:SER:OG 1:A:1728:ARG:N 2.52 0.431:B:2309:TYR:OH 1:B:2359:GLU:OE2 2.35 0.431:C:1726:SER:OG 1:C:1728:ARG:N 2.51 0.431:A:1289:PHE:HD1 1:A:1292:LEU:HD12 1.83 0.431:B:1671:ARG:HG2 1:B:1672:THR:HG23 2.00 0.431:A:1671:ARG:HG2 1:A:1672:THR:HG23 2.00 0.431:C:2388:LYS:HD2 1:C:2394:GLU:HG2 1.99 0.431:A:1211:ASP:HA 1:A:1214:ILE:HG12 2.00 0.431:B:1656:ILE:HB 1:B:1659:LEU:HD13 2.00 0.431:B:2285:GLN:HB3 1:B:2443:LEU:HG 1.99 0.431:C:2410:VAL:HG21 1:C:2427:LEU:HD12 2.01 0.431:C:2461:LEU:HD12 1:C:2463:GLY:H 1.83 0.431:A:2410:VAL:HG21 1:A:2427:LEU:HD12 2.01 0.431:A:593:MET:O 1:A:597:VAL:CB 2.66 0.431:B:1726:SER:OG 1:B:1728:ARG:N 2.52 0.43
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Page 19 Full wwPDB EM Validation Report EMD-6865, 5Z10
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Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)1:B:2388:LYS:HD2 1:B:2394:GLU:HG2 1.99 0.431:C:2037:LEU:HD13 1:C:2037:LEU:HA 1.83 0.431:C:841:PRO:HA 1:C:1105:SER:HB2 2.01 0.431:A:841:PRO:HA 1:A:1105:SER:HB2 2.01 0.43
1:B:2295:ARG:HG2 1:B:2295:ARG:H 1.65 0.431:C:1353:ARG:NE 1:C:2518:GLU:OE2 2.41 0.431:B:2397:ASP:OD1 1:B:2397:ASP:N 2.50 0.431:C:2397:ASP:N 1:C:2397:ASP:OD1 2.50 0.43
1:A:2208:LEU:HD23 1:A:2208:LEU:HA 1.82 0.431:A:2388:LYS:HD2 1:A:2394:GLU:HG2 2.00 0.431:B:971:ASP:HA 1:B:1150:LEU:HD11 1.99 0.431:B:1211:ASP:HA 1:B:1214:ILE:HG12 2.00 0.43
1:B:2461:LEU:HD12 1:B:2463:GLY:H 1.83 0.431:A:1727:LYS:HG3 1:A:1728:ARG:HG2 1.99 0.431:A:2229:THR:OG1 1:A:2239:PHE:O 2.32 0.431:B:2410:VAL:HG21 1:B:2427:LEU:HD12 2.01 0.431:A:2461:LEU:HD12 1:A:2463:GLY:H 1.83 0.421:C:593:MET:O 1:C:597:VAL:CB 2.66 0.421:B:2372:PHE:HZ 1:B:2446:MET:HB3 1.84 0.421:C:2491:SER:OG 1:C:2491:SER:O 2.34 0.42
1:C:2521:LEU:HD12 1:C:2521:LEU:HA 1.90 0.421:A:2131:LEU:HA 1:A:2131:LEU:HD12 1.83 0.421:A:2372:PHE:HZ 1:A:2446:MET:HB3 1.84 0.421:B:1402:ASP:OD1 1:B:1402:ASP:N 2.52 0.421:A:2307:GLU:O 1:A:2351:ARG:NH2 2.53 0.421:A:2427:LEU:HA 1:A:2427:LEU:HD23 1.87 0.42
1:A:2521:LEU:HD12 1:A:2521:LEU:HA 1.90 0.421:C:2372:PHE:HZ 1:C:2446:MET:HB3 1.84 0.421:A:1402:ASP:OD1 1:A:1402:ASP:N 2.52 0.421:A:2221:ASN:OD1 1:A:2325:ARG:NE 2.43 0.421:C:1211:ASP:HA 1:C:1214:ILE:HG12 2.00 0.421:C:1671:ARG:HG2 1:C:1672:THR:HG23 2.00 0.421:A:1401:LEU:HD12 1:C:2179:LYS:HE2 2.01 0.421:A:1656:ILE:HB 1:A:1659:LEU:HD13 2.00 0.421:B:1289:PHE:HD1 1:B:1292:LEU:HD12 1.83 0.421:B:1540:LEU:HD13 1:B:1559:LEU:HD13 2.02 0.421:B:2131:LEU:HA 1:B:2131:LEU:HD12 1.83 0.421:B:1727:LYS:H 1:B:1727:LYS:HG2 1.53 0.421:B:2307:GLU:O 1:B:2351:ARG:NH2 2.53 0.421:C:2065:LEU:HA 1:C:2065:LEU:HD12 1.92 0.421:C:2307:GLU:O 1:C:2351:ARG:NH2 2.52 0.42
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Page 20 Full wwPDB EM Validation Report EMD-6865, 5Z10
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Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)1:C:1656:ILE:HB 1:C:1659:LEU:HD13 2.00 0.421:A:1036:TYR:HA 1:A:1039:PHE:CE1 2.55 0.411:A:2308:LEU:HD22 1:A:2358:LEU:HD21 2.02 0.411:B:1541:LEU:O 1:B:1545:LEU:N 2.52 0.411:B:841:PRO:HA 1:B:1105:SER:HB2 2.01 0.41
1:A:2065:LEU:HD12 1:A:2065:LEU:HA 1.92 0.411:A:2088:ILE:H 1:A:2088:ILE:HG13 1.69 0.41
1:B:1036:TYR:HA 1:B:1039:PHE:CE1 2.55 0.411:B:2230:LEU:HB3 1:B:2239:PHE:HB3 2.03 0.411:C:2119:LEU:HD11 1:C:2164:ILE:HG23 2.03 0.41
1:B:2088:ILE:H 1:B:2088:ILE:HG13 1.69 0.411:B:703:GLN:O 1:B:707:PHE:N 2.53 0.411:C:1541:LEU:O 1:C:1545:LEU:N 2.52 0.411:C:703:GLN:O 1:C:707:PHE:N 2.53 0.41
1:A:1353:ARG:NE 1:A:2518:GLU:OE2 2.41 0.411:B:2491:SER:O 1:B:2491:SER:OG 2.34 0.41
1:A:2179:LYS:HE2 1:B:1401:LEU:HD12 2.01 0.411:C:1727:LYS:HG2 1:C:1727:LYS:H 1.53 0.411:A:2504:LEU:HD12 1:A:2504:LEU:HA 1.94 0.411:B:2179:LYS:HE2 1:C:1401:LEU:HD12 2.02 0.411:B:2378:ALA:HB3 1:B:2450:SER:HA 2.03 0.411:C:1540:LEU:HD13 1:C:1559:LEU:HD13 2.02 0.411:C:1551:VAL:HG22 1:C:1554:GLY:H 1.86 0.411:A:2037:LEU:HD13 1:A:2037:LEU:HA 1.83 0.411:B:2059:ILE:HD13 1:B:2059:ILE:HA 1.89 0.411:B:2352:ARG:HD3 1:B:2355:ALA:HB3 2.03 0.411:C:2308:LEU:HD22 1:C:2358:LEU:HD21 2.03 0.411:A:2020:PHE:HA 1:A:2023:MET:HE2 2.02 0.401:A:2119:LEU:HD11 1:A:2164:ILE:HG23 2.03 0.401:B:2119:LEU:HD11 1:B:2164:ILE:HG23 2.03 0.401:C:2208:LEU:HD23 1:C:2208:LEU:HA 1.82 0.401:C:2352:ARG:HD3 1:C:2355:ALA:HB3 2.03 0.401:C:2406:ARG:HD3 1:C:2406:ARG:HA 1.83 0.401:A:2352:ARG:HD3 1:A:2355:ALA:HB3 2.03 0.401:C:2504:LEU:HA 1:C:2504:LEU:HD12 1.94 0.40
1:A:1540:LEU:HD13 1:A:1559:LEU:HD13 2.02 0.401:B:2020:PHE:HA 1:B:2023:MET:HE2 2.02 0.401:B:2179:LYS:HD3 1:C:1401:LEU:HB2 2.04 0.401:A:1213:LEU:HA 1:A:1213:LEU:HD12 1.96 0.401:A:2230:LEU:HB3 1:A:2239:PHE:HB3 2.03 0.401:B:2289:SER:HA 1:B:2431:VAL:HG13 2.03 0.40
Continued on next page...
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Page 21 Full wwPDB EM Validation Report EMD-6865, 5Z10
Continued from previous page...
Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)1:C:1036:TYR:HA 1:C:1039:PHE:CE1 2.55 0.401:C:1402:ASP:N 1:C:1402:ASP:OD1 2.52 0.40
1:C:2230:LEU:HB3 1:C:2239:PHE:HB3 2.03 0.401:C:2361:ARG:HA 1:C:2362:PRO:HD3 1.99 0.401:A:1401:LEU:HB2 1:C:2179:LYS:HD3 2.04 0.401:A:1403:HIS:NE2 1:A:2523:GLU:OE2 2.55 0.401:A:1780:ASP:OD1 1:A:1780:ASP:N 2.48 0.401:A:2050:GLN:NE2 1:A:2093:SER:OG 2.47 0.401:B:1331:ILE:HD13 1:B:1331:ILE:HA 1.93 0.401:B:2321:TRP:HD1 1:B:2323:PHE:HE2 1.69 0.401:B:2308:LEU:HD22 1:B:2358:LEU:HD21 2.03 0.401:B:2477:VAL:HG13 1:C:2130:PHE:HZ 1.86 0.401:C:2059:ILE:HD13 1:C:2059:ILE:HA 1.89 0.401:C:2088:ILE:H 1:C:2088:ILE:HG13 1.68 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 PDB entries followed by that with respect to all EMentries.
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 1270/2547 (50%) 1168 (92%) 102 (8%) 0 100 100
1 B 1270/2547 (50%) 1168 (92%) 102 (8%) 0 100 100
1 C 1270/2547 (50%) 1168 (92%) 102 (8%) 0 100 100
All All 3810/7641 (50%) 3504 (92%) 306 (8%) 0 100 100
There are no Ramachandran outliers to report.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#torsion_angleshttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#protein_backbone
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5.3.2 Protein sidechains i○
In the following table, the Percentiles column shows the percent sidechain outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all EMentries.
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 883/2246 (39%) 876 (99%) 7 (1%) 81 88
1 B 883/2246 (39%) 876 (99%) 7 (1%) 81 88
1 C 883/2246 (39%) 876 (99%) 7 (1%) 81 88
All All 2649/6738 (39%) 2628 (99%) 21 (1%) 82 88
All (21) residues with a non-rotameric sidechain are listed below:
Mol Chain Res Type1 A 1178 SER1 A 1280 ILE1 A 1295 ARG1 A 1525 LYS1 A 1797 ARG1 A 2333 VAL1 A 2441 CYS1 B 1178 SER1 B 1280 ILE1 B 1295 ARG1 B 1525 LYS1 B 1797 ARG1 B 2333 VAL1 B 2441 CYS1 C 1178 SER1 C 1280 ILE1 C 1295 ARG1 C 1525 LYS1 C 1797 ARG1 C 2333 VAL1 C 2441 CYS
Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (34)such sidechains are listed below:
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#protein_sidechains
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Mol Chain Res Type1 A 1200 GLN1 A 1315 GLN1 A 1510 GLN1 A 1668 GLN1 A 1669 GLN1 A 1686 HIS1 A 2018 GLN1 A 2058 HIS1 A 2380 ASN1 A 2409 GLN1 A 2442 ASN1 B 1200 GLN1 B 1315 GLN1 B 1510 GLN1 B 1668 GLN1 B 1669 GLN1 B 1686 HIS1 B 2018 GLN1 B 2058 HIS1 B 2380 ASN1 B 2409 GLN1 B 2442 ASN1 C 1200 GLN1 C 1315 GLN1 C 1510 GLN1 C 1668 GLN1 C 1669 GLN1 C 1686 HIS1 C 1789 GLN1 C 2018 GLN1 C 2058 HIS1 C 2380 ASN1 C 2409 GLN1 C 2442 ASN
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.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#rnahttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#nonstandard_residues_and_ligands
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5.5 Carbohydrates i○
There are no monosaccharides in this entry.
5.6 Ligand geometry i○
There are no ligands in this entry.
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/EMValidationReportHelp#nonstandard_residues_and_ligandshttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#nonstandard_residues_and_ligandshttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#nonstandard_residues_and_ligandshttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#polymer_linkage
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Page 25 Full wwPDB EM Validation Report EMD-6865, 5Z10
6 Map visualisation i○
This section contains visualisations of the EMDB entry EMD-6865. These allow visual inspectionof the internal detail of the map and identification of artifacts.
No raw map or half-maps were deposited for this entry and therefore no images, graphs, etc.pertaining to the raw map can be shown.
6.1 Orthogonal projections i○
6.1.1 Primary map
X Y Z
The images above show the map projected in three orthogonal directions.
6.2 Central slices i○
6.2.1 Primary map
X Index: 140 Y Index: 140 Z Index: 140
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_visualisationhttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#orthogonal_projectionshttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#central_slices
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Page 26 Full wwPDB EM Validation Report EMD-6865, 5Z10
The images above show central slices of the map in three orthogonal directions.
6.3 Largest variance slices i○
6.3.1 Primary map
X Index: 142 Y Index: 143 Z Index: 178
The images above show the largest variance slices of the map in three orthogonal directions.
6.4 Orthogonal surface views i○
6.4.1 Primary map
X Y Z
The images above show the 3D surface view of the map at the recommended contour level 0.027.These images, in conjunction with the slice images, may facilitate assessment of whether an ap-propriate contour level has been provided.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#largest_variance_sliceshttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#orthogonal_views
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6.5 Mask visualisation i○
This section was not generated. No masks/segmentation were deposited.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#masks
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7 Map analysis i○
This section contains the results of statistical analysis of the map.
7.1 Map-value distribution i○
The map-value distribution is plotted in 128 intervals along the x-axis. The y-axis is logarithmic.A spike in this graph at zero usually indicates that the volume has been masked.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_analysishttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_value_distribution
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Page 29 Full wwPDB EM Validation Report EMD-6865, 5Z10
7.2 Volume estimate i○
The volume at the recommended contour level is 535 nm3; this corresponds to an approximatemass of 483 kDa.
The volume estimate graph shows how the enclosed volume varies with the contour level. Therecommended contour level is shown as a vertical line and the intersection between the line andthe curve gives the volume of the enclosed surface at the given level.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#volume_estimate
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Page 30 Full wwPDB EM Validation Report EMD-6865, 5Z10
7.3 Rotationally averaged power spectrum i○
*Reported resolution corresponds to spatial frequency of 0.252 Å−1
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#raps
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8 Fourier-Shell correlation i○
Fourier-Shell Correlation (FSC) is the most commonly used method to estimate the resolution ofsingle-particle and subtomogram-averaged maps. The shape of the curve depends on the imposedsymmetry, mask and whether or not the two 3D reconstructions used were processed from acommon reference. The reported resolution is shown as a black line. A curve is displayed for thehalf-bit criterion in addition to lines showing the 0.143 gold standard cut-off and 0.5 cut-off.
8.1 FSC i○
*Reported resolution corresponds to spatial frequency of 0.252 Å−1
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#fsc_validationhttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#fsc_validation
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8.2 Resolution estimates i○
Resolution estimate (Å) Estimation criterion (FSC cut-off)0.143 0.5 Half-bitReported by author 3.97 - -
Author-provided FSC curve 3.98 4.80 4.12Calculated* - - -
*Resolution estimate based on FSC curve calculated by comparison of deposited half-maps.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#resolution_estimates
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9 Map-model fit i○
This section contains information regarding the fit between EMDB map EMD-6865 and PDBmodel 5Z10. Per-residue inclusion information can be found in section 3 on page 4.
9.1 Map-model overlay i○
X Y Z
The images above show the 3D surface view of the map at the recommended contour level 0.027at 50% transparency in yellow overlaid with a ribbon representation of the model coloured in blue.These images allow for the visual assessment of the quality of fit between the atomic model andthe map.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_fithttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_overlay
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9.2 Atom inclusion i○
At the recommended contour level, 95% of all backbone atoms, 86% of all non-hydrogen atoms,are inside the map.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#atom_inclusion_by_contour
Overall quality at a glanceEntry compositionResidue-property plotsExperimental informationModel qualityStandard geometryToo-close contactsTorsion anglesProtein backboneProtein sidechainsRNA
Non-standard residues in protein, DNA, RNA chainsCarbohydratesLigand geometryOther polymersPolymer linkage issues
Map visualisationOrthogonal projectionsPrimary map
Central slicesPrimary map
Largest variance slicesPrimary map
Orthogonal surface viewsPrimary map
Mask visualisation
Map analysisMap-value distributionVolume estimateRotationally averaged power spectrum
Fourier-Shell correlationFSCResolution estimates
Map-model fitMap-model overlayAtom inclusion