Full wwPDB EM Validation Report i○

Apr 10, 2021 – 12:08 PM EDT

PDB ID : 7L7FEMDB ID : EMD-23211

Title : Cryo-EM structure of human ACE2 receptor bound to protein encoded byvaccine candidate BNT162b1

Authors : Lees, J.A.; Han, S.Deposited on : 2020-12-28

Resolution : 3.24 Å(reported)

This is a Full wwPDB EM 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/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.dev75MolProbity : 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) : 2.18

Page 2 Full wwPDB EM Validation Report EMD-23211, 7L7F

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 3.24 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 <=5%The upper red bar (where present) indicates the fraction of residues that have poor fit to the EMmap (all-atom inclusion < 40%). The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 B 805

1 D 805

2 E 266

2 F 266

Page 3 Full wwPDB EM Validation Report EMD-23211, 7L7F

2 Entry composition i○

There are 2 unique types of molecules in this entry. The entry contains 14542 atoms, of which 0are hydrogens 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 Angiotensin-converting enzyme 2.

Mol Chain Residues Atoms AltConf Trace

1 B 711 Total C N O S5809 3716 972 1088 33 0 0

1 D 711 Total C N O S5809 3716 972 1088 33 0 0

• Molecule 2 is a protein called Spike glycoprotein, Envelope glycoprotein fusion.

Mol Chain Residues Atoms AltConf Trace

2 E 183 Total C N O S1462 939 242 274 7 0 0

2 F 183 Total C N O S1462 939 242 274 7 0 0

There are 40 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceE 529 GLY - linker UNP P0DTC2E 530 SER - linker UNP P0DTC2E 531 PRO - linker UNP P0DTC2E 532 GLY - linker UNP P0DTC2E 533 SER - linker UNP P0DTC2E 534 GLY - linker UNP P0DTC2E 535 SER - linker UNP P0DTC2E 536 GLY - linker UNP P0DTC2E 537 SER - linker UNP P0DTC2E 566 ARG - expression tag UNP M1E1E4E 567 SER - expression tag UNP M1E1E4E 568 LEU - expression tag UNP M1E1E4E 569 GLU - expression tag UNP M1E1E4E 570 VAL - expression tag UNP M1E1E4E 571 LEU - expression tag UNP M1E1E4E 572 PHE - expression tag UNP M1E1E4E 573 GLN - expression tag UNP M1E1E4

Continued on next page...

Page 4 Full wwPDB EM Validation Report EMD-23211, 7L7F

Continued from previous page...Chain Residue Modelled Actual Comment Reference

E 574 GLY - expression tag UNP M1E1E4E 575 PRO - expression tag UNP M1E1E4E 576 GLY - expression tag UNP M1E1E4F 529 GLY - linker UNP P0DTC2F 530 SER - linker UNP P0DTC2F 531 PRO - linker UNP P0DTC2F 532 GLY - linker UNP P0DTC2F 533 SER - linker UNP P0DTC2F 534 GLY - linker UNP P0DTC2F 535 SER - linker UNP P0DTC2F 536 GLY - linker UNP P0DTC2F 537 SER - linker UNP P0DTC2F 566 ARG - expression tag UNP M1E1E4F 567 SER - expression tag UNP M1E1E4F 568 LEU - expression tag UNP M1E1E4F 569 GLU - expression tag UNP M1E1E4F 570 VAL - expression tag UNP M1E1E4F 571 LEU - expression tag UNP M1E1E4F 572 PHE - expression tag UNP M1E1E4F 573 GLN - expression tag UNP M1E1E4F 574 GLY - expression tag UNP M1E1E4F 575 PRO - expression tag UNP M1E1E4F 576 GLY - expression tag UNP M1E1E4

Page 5 Full wwPDB EM Validation Report EMD-23211, 7L7F

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: Angiotensin-converting enzyme 2

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Page 6 Full wwPDB EM Validation Report EMD-23211, 7L7F

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• Molecule 2: Spike glycoprotein, Envelope glycoprotein fusion

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• Molecule 2: Spike glycoprotein, Envelope glycoprotein fusion

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Page 7 Full wwPDB EM Validation Report EMD-23211, 7L7F

4 Experimental information i○

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C2 DepositorNumber of particles used 74784 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

) 52.51 DepositorMinimum defocus (nm) Not providedMaximum defocus (nm) Not providedMagnification Not providedImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 0.080 DepositorMinimum map value -0.046 DepositorAverage map value 0.000 DepositorMap value standard deviation 0.002 DepositorRecommended contour level 0.0159 DepositorMap size (Å) 391.5, 391.5, 391.5 wwPDBMap dimensions 450, 450, 450 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 0.87, 0.87, 0.87 Depositor

Page 8 Full wwPDB EM Validation Report EMD-23211, 7L7F

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| >5

1 B 0.31 0/5964 0.43 0/80911 D 0.31 0/5964 0.43 0/80912 E 0.29 0/1503 0.50 0/20432 F 0.29 0/1503 0.50 0/2043All All 0.31 0/14934 0.45 0/20268

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 B 5809 0 5600 71 01 D 5809 0 5600 71 02 E 1462 0 1383 28 02 F 1462 0 1383 27 0All All 14542 0 13966 195 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 7.

All (195) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Page 9 Full wwPDB EM Validation Report EMD-23211, 7L7F

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:B:524:GLN:NE2 1:B:580:ASN:H 1.42 1.161:D:524:GLN:NE2 1:D:580:ASN:H 1.42 1.151:D:327:PHE:HZ 1:D:358:ILE:HD12 1.21 1.051:B:327:PHE:HZ 1:B:358:ILE:HD12 1.22 1.04

2:F:350:VAL:HG12 2:F:422:ASN:HB3 1.46 0.962:E:350:VAL:HG12 2:E:422:ASN:HB3 1.46 0.941:B:524:GLN:HE22 1:B:580:ASN:H 1.16 0.921:B:385:TYR:HE1 1:B:393:ARG:HB3 1.37 0.891:B:327:PHE:CZ 1:B:358:ILE:HD12 2.08 0.88

1:D:524:GLN:HE22 1:D:580:ASN:H 1.17 0.881:D:327:PHE:CZ 1:D:358:ILE:HD12 2.08 0.881:D:385:TYR:HE1 1:D:393:ARG:HB3 1.37 0.871:D:524:GLN:NE2 1:D:580:ASN:N 2.27 0.801:B:524:GLN:NE2 1:B:580:ASN:N 2.27 0.781:D:429:GLN:HE21 1:D:430:GLU:HG3 1.49 0.772:E:379:CYS:HA 2:E:432:CYS:HB2 1.66 0.772:F:379:CYS:HA 2:F:432:CYS:HB2 1.66 0.76

1:B:429:GLN:HE21 1:B:430:GLU:HG3 1.49 0.761:D:385:TYR:CE1 1:D:393:ARG:HB3 2.21 0.761:D:524:GLN:HE21 1:D:580:ASN:H 1.34 0.761:B:524:GLN:HE21 1:B:580:ASN:H 1.34 0.751:B:385:TYR:CE1 1:B:393:ARG:HB3 2.21 0.741:D:524:GLN:HE22 1:D:580:ASN:N 1.88 0.711:D:429:GLN:HG3 1:D:430:GLU:H 1.56 0.711:B:524:GLN:HE22 1:B:580:ASN:N 1.87 0.701:B:435:GLU:OE2 1:B:540:HIS:NE2 2.19 0.701:B:429:GLN:HG3 1:B:430:GLU:H 1.56 0.702:F:336:CYS:HB3 2:F:337:PRO:HD3 1.74 0.702:E:336:CYS:HB3 2:E:337:PRO:HD3 1.74 0.681:D:435:GLU:OE2 1:D:540:HIS:NE2 2.19 0.662:E:461:LEU:HD12 2:E:465:GLU:HB3 1.77 0.661:B:288:LYS:NZ 1:B:433:GLU:OE1 2.30 0.651:D:288:LYS:NZ 1:D:433:GLU:OE1 2.30 0.65

2:F:461:LEU:HD12 2:F:465:GLU:HB3 1.78 0.641:B:327:PHE:HZ 1:B:358:ILE:CD1 2.06 0.631:B:385:TYR:HE1 1:B:393:ARG:CB 2.10 0.621:B:429:GLN:HG3 1:B:430:GLU:N 2.15 0.622:E:484:GLU:HG2 2:E:489:TYR:HA 1.82 0.621:B:653:GLN:OE1 1:D:638:ASN:ND2 2.33 0.621:D:385:TYR:HE1 1:D:393:ARG:CB 2.11 0.622:E:350:VAL:CG1 2:E:422:ASN:HB3 2.27 0.612:F:484:GLU:HG2 2:F:489:TYR:HA 1.81 0.61

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Page 10 Full wwPDB EM Validation Report EMD-23211, 7L7F

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Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:D:429:GLN:HG3 1:D:430:GLU:N 2.15 0.611:B:638:ASN:ND2 1:D:653:GLN:OE1 2.33 0.601:B:697:ARG:NH1 1:B:701:GLU:OE1 2.35 0.591:B:312:GLU:O 1:B:316:VAL:HG23 2.03 0.59

1:D:697:ARG:NH1 1:D:701:GLU:OE1 2.35 0.591:B:524:GLN:HE22 1:B:579:MET:HA 1.67 0.591:D:312:GLU:O 1:D:316:VAL:HG23 2.02 0.591:D:90:ASN:HB3 1:D:93:VAL:HG12 1.86 0.58

1:D:524:GLN:HE22 1:D:579:MET:HA 1.67 0.581:B:145:GLU:HB3 1:B:146:PRO:HD3 1.86 0.581:B:90:ASN:HB3 1:B:93:VAL:HG12 1.85 0.571:D:327:PHE:HZ 1:D:358:ILE:CD1 2.06 0.572:F:350:VAL:CG1 2:F:422:ASN:HB3 2.27 0.571:D:145:GLU:HB3 1:D:146:PRO:HD3 1.86 0.572:F:350:VAL:HG12 2:F:422:ASN:CB 2.29 0.571:B:621:ARG:HD3 1:B:678:ARG:HH11 1.70 0.561:D:621:ARG:HD3 1:D:678:ARG:HH11 1.70 0.562:F:371:SER:OG 2:F:372:ALA:N 2.39 0.561:B:327:PHE:CZ 1:B:358:ILE:CD1 2.86 0.552:E:371:SER:OG 2:E:372:ALA:N 2.39 0.54

1:B:503:LEU:HD12 1:B:504:PHE:H 1.73 0.541:D:269:ASP:OD2 1:D:269:ASP:N 2.38 0.541:D:503:LEU:HD12 1:D:504:PHE:H 1.73 0.542:F:379:CYS:CA 2:F:432:CYS:HB2 2.32 0.541:D:327:PHE:CZ 1:D:358:ILE:CD1 2.85 0.532:E:347:PHE:CE2 2:E:399:SER:HB2 2.43 0.532:E:350:VAL:HG12 2:E:422:ASN:CB 2.29 0.531:B:269:ASP:OD2 1:B:269:ASP:N 2.38 0.531:B:385:TYR:CE1 1:B:393:ARG:CA 2.92 0.532:F:347:PHE:CE2 2:F:399:SER:HB2 2.43 0.531:D:346:PRO:HA 1:D:359:LEU:O 2.09 0.531:B:346:PRO:HA 1:B:359:LEU:O 2.09 0.521:D:385:TYR:CE1 1:D:393:ARG:CA 2.92 0.522:F:358:ILE:HB 2:F:395:VAL:HG13 1.92 0.51

2:E:412:PRO:HB3 2:E:427:ASP:HA 1.93 0.512:F:412:PRO:HB3 2:F:427:ASP:HA 1.93 0.511:D:21:ILE:HG22 1:D:22:GLU:N 2.26 0.512:E:358:ILE:HB 2:E:395:VAL:HG13 1.92 0.51

1:D:406:GLU:OE1 1:D:518:ARG:NH2 2.44 0.511:B:21:ILE:HG22 1:B:22:GLU:N 2.26 0.501:B:287:GLN:N 1:B:287:GLN:OE1 2.45 0.50

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Page 11 Full wwPDB EM Validation Report EMD-23211, 7L7F

Continued from previous page...

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:B:121:ASN:O 1:B:125:THR:HG23 2.12 0.501:B:406:GLU:OE1 1:B:518:ARG:NH2 2.44 0.502:E:451:TYR:O 2:E:452:LEU:HD23 2.12 0.502:F:451:TYR:O 2:F:452:LEU:HD23 2.12 0.502:F:470:THR:O 2:F:470:THR:OG1 2.30 0.491:D:23:GLU:O 1:D:27:THR:HG23 2.13 0.491:D:121:ASN:O 1:D:125:THR:HG23 2.12 0.491:B:23:GLU:O 1:B:27:THR:HG23 2.13 0.492:F:398:ASP:N 2:F:398:ASP:OD1 2.44 0.491:B:548:THR:O 1:B:548:THR:HG22 2.13 0.491:B:615:ASP:N 1:B:615:ASP:OD1 2.46 0.491:D:287:GLN:N 1:D:287:GLN:OE1 2.45 0.491:D:615:ASP:N 1:D:615:ASP:OD1 2.46 0.492:E:470:THR:O 2:E:470:THR:OG1 2.30 0.492:E:398:ASP:N 2:E:398:ASP:OD1 2.44 0.48

1:D:429:GLN:NE2 1:D:430:GLU:HG3 2.24 0.482:E:383:SER:HB2 2:E:386:LYS:CG 2.44 0.482:F:376:THR:HG22 2:F:378:LYS:HG3 1.96 0.482:E:516:GLU:N 2:E:516:GLU:OE2 2.47 0.471:D:429:GLN:CG 1:D:430:GLU:H 2.25 0.472:F:383:SER:HB2 2:F:386:LYS:CG 2.43 0.472:F:516:GLU:N 2:F:516:GLU:OE2 2.47 0.471:B:429:GLN:CG 1:B:430:GLU:H 2.25 0.47

1:D:548:THR:HG22 1:D:548:THR:O 2.13 0.471:B:385:TYR:CE1 1:B:393:ARG:HA 2.50 0.471:D:329:GLU:OE1 1:D:329:GLU:N 2.48 0.472:E:379:CYS:CA 2:E:432:CYS:HB2 2.32 0.461:B:385:TYR:CE1 1:B:393:ARG:CB 2.91 0.462:E:431:GLY:O 2:E:432:CYS:HB3 2.14 0.46

2:E:376:THR:HG22 2:E:378:LYS:HG3 1.96 0.461:B:429:GLN:NE2 1:B:430:GLU:HG3 2.24 0.461:B:620:VAL:O 1:B:680:SER:HA 2.16 0.46

1:D:385:TYR:CE1 1:D:393:ARG:CB 2.92 0.461:D:620:VAL:O 1:D:680:SER:HA 2.16 0.462:F:431:GLY:O 2:F:432:CYS:HB3 2.14 0.46

1:D:385:TYR:CE1 1:D:393:ARG:HA 2.51 0.451:B:450:LEU:HB2 1:B:451:PRO:HD3 1.98 0.451:B:75:GLU:O 1:B:78:THR:HG22 2.17 0.45

1:B:54:ILE:HD11 1:B:343:VAL:HG13 1.99 0.452:E:383:SER:HB2 2:E:386:LYS:HD2 1.99 0.451:D:39:LEU:HD23 1:D:39:LEU:HA 1.78 0.44

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Page 12 Full wwPDB EM Validation Report EMD-23211, 7L7F

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Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:D:187:LYS:HD2 1:D:199:TYR:CZ 2.52 0.441:D:685:VAL:HG12 1:D:686:THR:N 2.31 0.441:B:21:ILE:CG2 1:B:22:GLU:N 2.80 0.441:B:329:GLU:N 1:B:329:GLU:OE1 2.48 0.44

1:D:450:LEU:HB2 1:D:451:PRO:HD3 1.98 0.442:F:383:SER:HB2 2:F:386:LYS:HD2 2.00 0.441:B:685:VAL:HG12 1:B:686:THR:N 2.31 0.441:B:54:ILE:HB 1:B:341:LYS:HB2 2.00 0.44

1:B:187:LYS:HD2 1:B:199:TYR:CZ 2.52 0.441:B:305:GLN:O 1:B:309:LYS:HG2 2.18 0.44

2:E:467:ASP:OD1 2:E:468:ILE:N 2.51 0.441:D:75:GLU:O 1:D:78:THR:HG22 2.16 0.441:D:54:ILE:HB 1:D:341:LYS:HB2 2.00 0.441:D:305:GLN:O 1:D:309:LYS:HG2 2.18 0.441:D:21:ILE:CG2 1:D:22:GLU:N 2.81 0.442:F:467:ASP:OD1 2:F:468:ILE:N 2.51 0.441:B:218:SER:OG 1:B:219:ARG:N 2.51 0.431:D:235:PRO:O 1:D:239:HIS:HD2 2.01 0.43

1:B:370:LEU:HD21 1:B:413:ALA:HB2 1.99 0.431:B:476:LYS:HE3 1:B:476:LYS:HB3 1.87 0.432:E:350:VAL:CG1 2:E:422:ASN:CB 2.93 0.431:D:54:ILE:HD11 1:D:343:VAL:HG13 1.99 0.431:D:370:LEU:HD21 1:D:413:ALA:HB2 1.99 0.431:D:582:ARG:HH21 1:D:586:ASN:HD21 1.67 0.431:B:307:ILE:HG23 1:B:369:PHE:HD1 1.84 0.432:E:420:ASP:HB3 2:E:460:ASN:HB3 2.01 0.431:D:22:GLU:N 1:D:22:GLU:OE1 2.52 0.43

1:D:64:ASN:OD1 1:D:65:ALA:N 2.52 0.431:B:235:PRO:O 1:B:239:HIS:HD2 2.01 0.421:B:429:GLN:CG 1:B:430:GLU:N 2.82 0.421:D:307:ILE:HG23 1:D:369:PHE:HD1 1.84 0.421:D:293:VAL:O 1:D:293:VAL:HG23 2.20 0.42

2:F:383:SER:HB2 2:F:386:LYS:HG3 2.01 0.421:B:22:GLU:N 1:B:22:GLU:OE1 2.52 0.42

1:B:64:ASN:OD1 1:B:65:ALA:N 2.52 0.421:D:218:SER:OG 1:D:219:ARG:N 2.51 0.421:D:295:ASP:HA 1:D:298:VAL:HG22 2.01 0.422:F:350:VAL:CG1 2:F:422:ASN:CB 2.93 0.421:B:385:TYR:HE1 1:B:393:ARG:CA 2.31 0.421:B:582:ARG:HH21 1:B:586:ASN:HD21 1.67 0.421:D:148:LEU:HD23 1:D:148:LEU:HA 1.88 0.42

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Page 13 Full wwPDB EM Validation Report EMD-23211, 7L7F

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Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:D:689:LYS:HE3 1:D:689:LYS:HB2 1.81 0.421:B:542:CYS:SG 1:B:543:ASP:N 2.92 0.421:B:699:GLU:H 1:B:699:GLU:HG2 1.72 0.421:B:295:ASP:HA 1:B:298:VAL:HG22 2.01 0.42

1:B:439:LEU:HD23 1:B:439:LEU:HA 1.87 0.421:D:542:CYS:SG 1:D:543:ASP:N 2.92 0.422:E:516:GLU:O 2:E:517:LEU:HD12 2.20 0.421:D:476:LYS:HB3 1:D:476:LYS:HE3 1.87 0.412:F:420:ASP:HB3 2:F:460:ASN:HB3 2.01 0.411:B:293:VAL:O 1:B:293:VAL:HG23 2.20 0.41

2:F:399:SER:HB3 2:F:511:VAL:HG22 2.03 0.412:F:516:GLU:O 2:F:517:LEU:HD12 2.20 0.41

2:E:383:SER:HB2 2:E:386:LYS:HG3 2.01 0.411:D:474:MET:HE1 1:D:499:ASP:CG 2.41 0.411:B:148:LEU:HD23 1:B:148:LEU:HA 1.88 0.411:B:582:ARG:NH2 1:B:586:ASN:HD21 2.19 0.412:F:439:ASN:O 2:F:443:SER:OG 2.39 0.41

1:B:424:LEU:HD23 1:B:424:LEU:HA 1.84 0.411:D:344:CYS:SG 1:D:361:CYS:N 2.94 0.411:D:385:TYR:CD1 1:D:393:ARG:HA 2.56 0.411:D:459:TRP:O 1:D:463:VAL:HG23 2.21 0.41

2:E:493:GLN:HE21 2:E:493:GLN:HB3 1.71 0.411:D:596:LYS:HE3 1:D:596:LYS:HB2 1.87 0.412:E:399:SER:HB3 2:E:511:VAL:HG22 2.03 0.402:E:439:ASN:O 2:E:443:SER:OG 2.39 0.401:B:459:TRP:O 1:B:463:VAL:HG23 2.21 0.40

1:D:582:ARG:NH2 1:D:586:ASN:HD21 2.19 0.401:D:693:ASP:OD1 1:D:694:ILE:N 2.55 0.401:B:344:CYS:SG 1:B:361:CYS:N 2.94 0.401:B:693:ASP:OD1 1:B:694:ILE:N 2.55 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.

Page 14 Full wwPDB EM Validation Report EMD-23211, 7L7F

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 B 709/805 (88%) 661 (93%) 48 (7%) 0 100 100

1 D 709/805 (88%) 660 (93%) 49 (7%) 0 100 100

2 E 181/266 (68%) 156 (86%) 25 (14%) 0 100 100

2 F 181/266 (68%) 156 (86%) 25 (14%) 0 100 100

All All 1780/2142 (83%) 1633 (92%) 147 (8%) 0 100 100

There are no Ramachandran outliers to report.

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 B 630/711 (89%) 625 (99%) 5 (1%) 81 91

1 D 630/711 (89%) 625 (99%) 5 (1%) 81 91

2 E 159/227 (70%) 157 (99%) 2 (1%) 69 85

2 F 159/227 (70%) 157 (99%) 2 (1%) 69 85

All All 1578/1876 (84%) 1564 (99%) 14 (1%) 79 89

All (14) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 B 133 CYS1 B 138 PRO1 B 199 TYR1 B 381 TYR1 B 440 LEU2 E 432 CYS2 E 495 TYR1 D 133 CYS1 D 138 PRO1 D 199 TYR

Continued on next page...

Page 15 Full wwPDB EM Validation Report EMD-23211, 7L7F

Continued from previous page...Mol Chain Res Type1 D 381 TYR1 D 440 LEU2 F 432 CYS2 F 495 TYR

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (36)such sidechains are listed below:

Mol Chain Res Type1 B 102 GLN1 B 154 ASN1 B 239 HIS1 B 330 ASN1 B 340 GLN1 B 380 GLN1 B 394 ASN1 B 429 GLN1 B 437 ASN1 B 442 GLN1 B 524 GLN1 B 586 ASN1 B 599 ASN1 B 601 ASN2 E 360 ASN2 E 370 ASN2 E 493 GLN2 E 501 ASN1 D 102 GLN1 D 154 ASN1 D 239 HIS1 D 330 ASN1 D 340 GLN1 D 380 GLN1 D 394 ASN1 D 429 GLN1 D 437 ASN1 D 442 GLN1 D 524 GLN1 D 586 ASN1 D 599 ASN1 D 601 ASN2 F 360 ASN2 F 370 ASN

Continued on next page...

Page 16 Full wwPDB EM Validation Report EMD-23211, 7L7F

Continued from previous page...Mol Chain Res Type2 F 493 GLN2 F 501 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.

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.

Page 17 Full wwPDB EM Validation Report EMD-23211, 7L7F

6 Map visualisation i○

This section contains visualisations of the EMDB entry EMD-23211. 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: 225 Y Index: 225 Z Index: 225

Page 18 Full wwPDB EM Validation Report EMD-23211, 7L7F

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: 228 Y Index: 184 Z Index: 239

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 0.0159.These images, in conjunction with the slice images, may facilitate assessment of whether an ap-propriate contour level has been provided.

Page 19 Full wwPDB EM Validation Report EMD-23211, 7L7F

6.5 Mask visualisation i○

This section was not generated. No masks/segmentation were deposited.

Page 20 Full wwPDB EM Validation Report EMD-23211, 7L7F

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.

Page 21 Full wwPDB EM Validation Report EMD-23211, 7L7F

7.2 Volume estimate i○

The volume at the recommended contour level is 68 nm3; this corresponds to an approximate massof 62 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.

Page 22 Full wwPDB EM Validation Report EMD-23211, 7L7F

7.3 Rotationally averaged power spectrum i○

*Reported resolution corresponds to spatial frequency of 0.309 Å−1

Page 23 Full wwPDB EM Validation Report EMD-23211, 7L7F

8 Fourier-Shell correlation i○

This section was not generated. No FSC curve or half-maps provided.

Page 24 Full wwPDB EM Validation Report EMD-23211, 7L7F

9 Map-model fit i○

This section contains information regarding the fit between EMDB map EMD-23211 and PDBmodel 7L7F. Per-residue inclusion information can be found in section 3 on page 5.

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 0.0159at 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.

Page 25 Full wwPDB EM Validation Report EMD-23211, 7L7F

9.2 Atom inclusion i○

At the recommended contour level, 74% of all backbone atoms, 68% of all non-hydrogen atoms,are inside the map.