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Full wwPDB X-ray Structure Validation Report iO
May 14, 2020 � 08:00 pm BST
PDB ID : 4V8ATitle : The structure of thermorubin in complex with the 70S ribosome from Thermus
thermophilus.Authors : Bulkley, D.; Johnson, F.A.; Steitz, T.A.
Deposited on : 2011-12-05Resolution : 3.20 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] 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 : 2.11
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) : 2.11
https://www.wwpdb.org/validation/2017/XrayValidationReportHelphttps://www.wwpdb.org/validation/2017/XrayValidationReportHelphttps://www.wwpdb.org/validation/2017/XrayValidationReportHelphttps://www.wwpdb.org/validation/2017/XrayValidationReportHelp#references
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Page 2 Full wwPDB X-ray Structure Validation Report 4V8A
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 3.20 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.
MetricWhole archive(#Entries)
Similar resolution(#Entries, resolution range(Å))
Rfree 130704 1133 (3.20-3.20)Clashscore 141614 1253 (3.20-3.20)
Ramachandran outliers 138981 1234 (3.20-3.20)Sidechain outliers 138945 1233 (3.20-3.20)RSRZ outliers 127900 1095 (3.20-3.20)RNA backbone 3102 1010 (3.50-2.90)
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
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Page 3 Full wwPDB X-ray Structure Validation Report 4V8A
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Mol Chain Length Quality of chain
3 AD 276
3 BD 276
4 AE 206
4 BE 206
5 AF 205
5 BF 205
6 AG 182
6 BG 182
7 AH 180
7 BH 180
8 AI 148
8 BI 148
9 AN 140
9 BN 140
10 AO 122
10 BO 122
11 AP 150
11 BP 150
12 AQ 141
12 BQ 141
13 AR 118
13 BR 118
14 AS 112
14 BS 112
15 AT 146Continued on next page...
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Page 4 Full wwPDB X-ray Structure Validation Report 4V8A
Continued from previous page...
Mol Chain Length Quality of chain
15 BT 146
16 AU 118
16 BU 118
17 AV 101
17 BV 101
18 AW 113
18 BW 113
19 AX 96
19 BX 96
20 AY 110
20 BY 110
21 AZ 206
21 BZ 206
22 A0 85
22 B0 85
23 A1 98
23 B1 98
24 A2 72
24 B2 72
25 A3 60
25 B3 60
26 A4 71
26 B4 71
27 A5 60
27 B5 60Continued on next page...
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Page 5 Full wwPDB X-ray Structure Validation Report 4V8A
Continued from previous page...
Mol Chain Length Quality of chain
28 A6 54
28 B6 54
29 A7 49
29 B7 49
30 A8 65
30 B8 65
31 CA 1521
31 DA 1521
32 CB 256
32 DB 256
33 CC 239
33 DC 239
34 CD 209
34 DD 209
35 CE 162
35 DE 162
36 CF 101
36 DF 101
37 CG 156
37 DG 156
38 CH 138
38 DH 138
39 CI 128
39 DI 128
40 CJ 105Continued on next page...
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Page 6 Full wwPDB X-ray Structure Validation Report 4V8A
Continued from previous page...
Mol Chain Length Quality of chain
40 DJ 105
41 CK 129
41 DK 129
42 CL 132
42 DL 132
43 CM 126
43 DM 126
44 CN 61
44 DN 61
45 CO 89
45 DO 89
46 CP 88
46 DP 88
47 CQ 105
47 DQ 105
48 CR 88
48 DR 88
49 CS 93
49 DS 93
50 CT 106
50 DT 106
51 CU 27
51 DU 27
The following table lists non-polymeric compounds, carbohydrate monomers and non-standardresidues in protein, DNA, RNA chains that are outliers for geometric or electron-density-�t crite-ria:
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Page 7 Full wwPDB X-ray Structure Validation Report 4V8A
Mol Type Chain Res Chirality Geometry Clashes Electron density52 T8B AA 3001 - - X -52 T8B BA 3001 - - X -
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Page 8 Full wwPDB X-ray Structure Validation Report 4V8A
2 Entry composition iO
There are 53 unique types of molecules in this entry. The entry contains 279316 atoms, of which0 are 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 RNA chain called 23S ribosomal RNA.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
1 AA 2827Total C N O P60900 27102 11403 19569 2826
0 0 0
1 BA 2827Total C N O P60900 27102 11403 19569 2826
0 0 0
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceAA 272A G U CONFLICT GB AP008226.1BA 272A G U CONFLICT GB AP008226.1
Molecule 2 is a RNA chain called 5S ribosomal RNA.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
2 AB 120Total C N O P2574 1146 476 833 119
0 0 0
2 BB 120Total C N O P2574 1146 476 833 119
0 0 0
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceAB 120 G A CONFLICT GB AP008226.1BB 120 G A CONFLICT GB AP008226.1
Molecule 3 is a protein called 50S ribosomal protein L2.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
3 AD 275Total C N O S2136 1349 423 361 3
0 0 0
3 BD 275Total C N O S2136 1349 423 361 3
0 0 0
https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#entry_composition
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Page 9 Full wwPDB X-ray Structure Validation Report 4V8A
Molecule 4 is a protein called 50S ribosomal protein L3.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
4 AE 204Total C N O S1555 982 297 270 6
0 0 0
4 BE 204Total C N O S1555 982 297 270 6
0 0 0
Molecule 5 is a protein called 50S ribosomal protein L4.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
5 AF 203Total C N O S1576 1005 297 272 2
0 0 1
5 BF 203Total C N O S1576 1005 297 272 2
0 0 1
Molecule 6 is a protein called 50S ribosomal protein L5.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
6 AG 181Total C N O S1368 879 242 244 3
0 0 0
6 BG 181Total C N O S1368 879 242 244 3
0 0 0
Molecule 7 is a protein called 50S ribosomal protein L6.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
7 AH 174Total C N O S1317 837 243 236 1
0 0 0
7 BH 174Total C N O S1317 837 243 236 1
0 0 0
Molecule 8 is a protein called 50S ribosomal protein L9.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
8 AI 145Total C N O S1046 674 180 191 1
0 0 0
8 BI 145Total C N O S1046 674 180 191 1
0 0 0
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceAI 110 GLU ASP CONFLICT UNP Q5SLQ1
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Page 10 Full wwPDB X-ray Structure Validation Report 4V8A
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Chain Residue Modelled Actual Comment ReferenceBI 110 GLU ASP CONFLICT UNP Q5SLQ1
Molecule 9 is a protein called 50S ribosomal protein L13.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
9 AN 140Total C N O S1112 717 207 184 4
0 0 0
9 BN 140Total C N O S1112 717 207 184 4
0 0 0
Molecule 10 is a protein called 50S ribosomal protein L14.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
10 AO 122Total C N O S923 583 168 168 4
0 0 0
10 BO 122Total C N O S923 583 168 168 4
0 0 0
Molecule 11 is a protein called 50S ribosomal protein L15.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
11 AP 147Total C N O S1119 695 227 194 3
0 0 0
11 BP 147Total C N O S1119 695 227 194 3
0 0 0
Molecule 12 is a protein called 50S ribosomal protein L16.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
12 AQ 141Total C N O S1122 715 212 188 7
0 0 0
12 BQ 141Total C N O S1122 715 212 188 7
0 0 0
Molecule 13 is a protein called 50S ribosomal protein L17.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
13 AR 118Total C N O S968 604 203 160 1
0 0 0
13 BR 118Total C N O S968 604 203 160 1
0 0 0
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Page 11 Full wwPDB X-ray Structure Validation Report 4V8A
Molecule 14 is a protein called 50S ribosomal protein L18.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
14 AS 110Total C N O865 544 172 149
0 0 0
14 BS 110Total C N O865 544 172 149
0 0 0
Molecule 15 is a protein called 50S ribosomal protein L19.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
15 AT 131Total C N O S1063 666 213 183 1
0 0 0
15 BT 131Total C N O S1063 666 213 183 1
0 0 0
Molecule 16 is a protein called 50S ribosomal protein L20.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
16 AU 116Total C N O S959 608 201 149 1
0 0 0
16 BU 116Total C N O S959 608 201 149 1
0 0 0
Molecule 17 is a protein called 50S ribosomal protein L21.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
17 AV 101Total C N O S771 495 140 135 1
0 0 0
17 BV 101Total C N O S771 495 140 135 1
0 0 0
Molecule 18 is a protein called 50S ribosomal protein L22.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
18 AW 112Total C N O S881 554 172 153 2
0 0 0
18 BW 112Total C N O S881 554 172 153 2
0 0 0
Molecule 19 is a protein called 50S ribosomal protein L23.
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Page 12 Full wwPDB X-ray Structure Validation Report 4V8A
Mol Chain Residues Atoms ZeroOcc AltConf Trace
19 AX 95Total C N O S742 483 134 124 1
0 0 0
19 BX 95Total C N O S742 483 134 124 1
0 0 0
Molecule 20 is a protein called 50S ribosomal protein L24.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
20 AY 107Total C N O S785 503 145 131 6
0 0 0
20 BY 107Total C N O S785 503 145 131 6
0 0 0
Molecule 21 is a protein called 50S ribosomal protein L25.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
21 AZ 198Total C N O S1522 972 269 279 2
0 0 0
21 BZ 198Total C N O S1522 972 269 279 2
0 0 0
Molecule 22 is a protein called 50S ribosomal protein L27.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
22 A0 76Total C N O S594 368 125 100 1
0 0 0
22 B0 76Total C N O S594 368 125 100 1
0 0 0
Molecule 23 is a protein called 50S ribosomal protein L28.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
23 A1 97Total C N O S745 469 144 131 1
0 0 0
23 B1 97Total C N O S745 469 144 131 1
0 0 0
Molecule 24 is a protein called 50S ribosomal protein L29.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
24 A2 70Total C N O S588 365 118 103 2
0 0 0
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Page 13 Full wwPDB X-ray Structure Validation Report 4V8A
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Mol Chain Residues Atoms ZeroOcc AltConf Trace
24 B2 70Total C N O S588 365 118 103 2
0 0 0
Molecule 25 is a protein called 50S ribosomal protein L30.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
25 A3 59Total C N O458 293 87 78
0 0 0
25 B3 59Total C N O458 293 87 78
0 0 0
Molecule 26 is a protein called 50S ribosomal protein L31.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
26 A4 46Total C N O S349 223 57 64 5
0 0 0
26 B4 46Total C N O S349 223 57 64 5
0 0 0
Molecule 27 is a protein called 50S ribosomal protein L32.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
27 A5 59Total C N O S455 286 90 74 5
0 0 0
27 B5 59Total C N O S455 286 90 74 5
0 0 0
Molecule 28 is a protein called 50S ribosomal protein L33.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
28 A6 53Total C N O S449 278 90 77 4
0 0 0
28 B6 53Total C N O S449 278 90 77 4
0 0 0
Molecule 29 is a protein called 50S ribosomal protein L34.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
29 A7 48Total C N O S418 257 104 55 2
0 0 0
29 B7 48Total C N O S418 257 104 55 2
0 0 0
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Page 14 Full wwPDB X-ray Structure Validation Report 4V8A
Molecule 30 is a protein called 50S ribosomal protein L35.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
30 A8 64Total C N O S509 326 99 82 2
0 0 0
30 B8 64Total C N O S509 326 99 82 2
0 0 0
Molecule 31 is a RNA chain called 16S ribosomal RNA.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
31 CA 1498Total C N O P32208 14334 5974 10402 1498
0 0 0
31 DA 1498Total C N O P32208 14334 5974 10402 1498
0 0 0
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceCA ? - U DELETION GB AP008226.1DA ? - U DELETION GB AP008226.1
Molecule 32 is a protein called 30S ribosomal protein S2.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
32 CB 229Total C N O S1777 1134 318 320 5
0 0 0
32 DB 229Total C N O S1777 1134 318 320 5
0 0 0
Molecule 33 is a protein called 30S ribosomal protein S3.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
33 CC 206Total C N O S1450 906 279 264 1
0 0 0
33 DC 206Total C N O S1450 906 279 264 1
0 0 0
Molecule 34 is a protein called 30S ribosomal protein S4.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
34 CD 208Total C N O S1520 960 283 272 5
0 0 0
Continued on next page...
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Page 15 Full wwPDB X-ray Structure Validation Report 4V8A
Continued from previous page...
Mol Chain Residues Atoms ZeroOcc AltConf Trace
34 DD 208Total C N O S1520 960 283 272 5
0 0 0
Molecule 35 is a protein called 30S ribosomal protein S5.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
35 CE 148Total C N O S1105 699 204 198 4
0 0 0
35 DE 148Total C N O S1105 699 204 198 4
0 0 0
Molecule 36 is a protein called 30S ribosomal protein S6.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
36 CF 100Total C N O S781 495 137 146 3
0 0 0
36 DF 100Total C N O S781 495 137 146 3
0 0 0
Molecule 37 is a protein called 30S ribosomal protein S7.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
37 CG 155Total C N O S1167 727 224 210 6
0 0 0
37 DG 155Total C N O S1167 727 224 210 6
0 0 0
Molecule 38 is a protein called 30S ribosomal protein S8.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
38 CH 138Total C N O S1045 665 188 190 2
0 0 0
38 DH 138Total C N O S1045 665 188 190 2
0 0 0
Molecule 39 is a protein called 30S ribosomal protein S9.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
39 CI 125Total C N O852 533 163 156
0 0 0
39 DI 125Total C N O852 533 163 156
0 0 0
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Page 16 Full wwPDB X-ray Structure Validation Report 4V8A
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceCI 58 ARG HIS CONFLICT UNP P80374DI 58 ARG HIS CONFLICT UNP P80374
Molecule 40 is a protein called 30S ribosomal protein S10.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
40 CJ 96Total C N O659 408 131 120
0 0 0
40 DJ 96Total C N O659 408 131 120
0 0 0
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceCJ 75 LEU ILE CONFLICT UNP Q5SHN7DJ 75 LEU ILE CONFLICT UNP Q5SHN7
Molecule 41 is a protein called 30S ribosomal protein S11.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
41 CK 114Total C N O S828 516 155 154 3
0 0 0
41 DK 114Total C N O S828 516 155 154 3
0 0 0
Molecule 42 is a protein called 30S ribosomal protein S12.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
42 CL 122Total C N O S909 570 179 159 1
0 0 0
42 DL 122Total C N O S909 570 179 159 1
0 0 0
Molecule 43 is a protein called 30S ribosomal protein S13.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
43 CM 114Total C N O S801 494 164 142 1
0 0 0
43 DM 114Total C N O S801 494 164 142 1
0 0 0
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Page 17 Full wwPDB X-ray Structure Validation Report 4V8A
Molecule 44 is a protein called 30S ribosomal protein S14.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
44 CN 60Total C N O S478 303 99 72 4
0 0 0
44 DN 60Total C N O S478 303 99 72 4
0 0 0
Molecule 45 is a protein called 30S ribosomal protein S15.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
45 CO 88Total C N O S724 453 143 126 2
0 0 0
45 DO 88Total C N O S724 453 143 126 2
0 0 0
Molecule 46 is a protein called 30S ribosomal protein S16.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
46 CP 82Total C N O S651 416 123 111 1
0 0 0
46 DP 82Total C N O S651 416 123 111 1
0 0 0
Molecule 47 is a protein called 30S ribosomal protein S17.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
47 CQ 99Total C N O S823 528 151 142 2
0 0 0
47 DQ 99Total C N O S823 528 151 142 2
0 0 0
Molecule 48 is a protein called 30S ribosomal protein S18.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
48 CR 68Total C N O514 329 98 87
0 0 0
48 DR 68Total C N O514 329 98 87
0 0 0
Molecule 49 is a protein called 30S ribosomal protein S19.
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Page 18 Full wwPDB X-ray Structure Validation Report 4V8A
Mol Chain Residues Atoms ZeroOcc AltConf Trace
49 CS 78Total C N O S544 342 105 95 2
0 0 0
49 DS 78Total C N O S544 342 105 95 2
0 0 0
Molecule 50 is a protein called 30S ribosomal protein S20.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
50 CT 96Total C N O S708 435 151 120 2
0 0 0
50 DT 96Total C N O S708 435 151 120 2
0 0 0
Molecule 51 is a protein called 30S ribosomal protein THX.
Mol Chain Residues Atoms ZeroOcc AltConf Trace
51 CU 23Total C N O199 122 48 29
0 0 0
51 DU 23Total C N O199 122 48 29
0 0 0
Molecule 52 is Thermorubin (three-letter code: T8B) (formula: C32H24O12).
Mol Chain Residues Atoms ZeroOcc AltConf
52 AA 1Total C O44 32 12
0 0
Continued on next page...
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Page 19 Full wwPDB X-ray Structure Validation Report 4V8A
Continued from previous page...
Mol Chain Residues Atoms ZeroOcc AltConf
52 BA 1Total C O44 32 12
0 0
Molecule 53 is MAGNESIUM ION (three-letter code: MG) (formula: Mg).
Mol Chain Residues Atoms ZeroOcc AltConf
53 AA 2Total Mg2 2
0 0
53 BA 2Total Mg2 2
0 0
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Page 20 Full wwPDB X-ray Structure Validation Report 4V8A
3 Residue-property plots iO
These plots are drawn for all protein, RNA and DNA chains in the entry. The �rst 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 geometry and 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 �t 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: 23S ribosomal RNA
Chain AA:
G U C A A6
G7
A8
U9
G10
G11•
U12
A13
A14
G15
G16
G17
C18
C19
C20
G23
G24
U25
G26
G27
A28
U29
G30
C31
C34
G35
G36
C39
C40
C41
C45
C47
G51
A52
A53
G54
G55
A56
C57
G58
U59
G60
G61
C62
U63
A64
C69
G70
A71
U72
A73
A74
G75
C76
C77
A78
G81
G82
G83
A84
G85
C86
C87
G88
G89
U90
A92
G93
C94
G94A
G95
G96
G100
G102
A103
U104
C107
U108
G109
G110
A111
U112
G113
U114
C115
C116
G117
A118
A119
U120
G121
G124
G125
A126
A127
C128
C129
C130
G131
G139A
G140
A141
A142
C142A
G143
C143A
G146
U147
G154
C154A
U U U U G171
C172
G175
G176
G177
G178
G179
G180
A181
A182
C183
C184
U185
G186
G187
G188
G189
A190
A191
C192
U193
G194
A195
A196
A197
C198
A199
U200
C201
U202
C203
A204
G205
U206
A207
C208
C209
C210
A211
G212
A213
G214
G215
A216
G217
A218
A221
A222
A223
G224
A225
G226
A227
A228
A229•
U230
A233
C236
C237
C238
U239
G240
U243
A244
G247
G248
C249
G250
A251
G252
A255
A256
C263
C264
A265
G266
C271C
G271D
U271E
C271F
C271G
G271H
G271I
C271J
U271K
U271L
G271M
U271N
C271O
C271P
G271Q
G271R
G271V
G272B
G272C
C272H
U272I
C272J•
G274
G275•
A C A278
C279•
C280
U284
C285
C286
C287
C288
A289
G290
C296
C297
G298
A299
A300
G301
C302
A310
A311
G312
G315
C316
G317
C318
C319
A320
G321
A322
G323
A324
G325
G326
G327
U328
G329
A330
A331
A332
G333
C334
C335
C336
C337
A340
G341
G342
C343
G344
A345
A346
G351
G352
G353
G354
G355
A359
G360
G361
U362
G363
A363A
G363B
G363C
G363D
U363E
A363F
C366
G370
A371
G372
U373
A374
C375
C376
U384
C385
G386
G389
A390
G391
C392
C393
A394
G399
G400
A401
A402
U403
C404
U405
G406
C409
G410
G411
A412
C413
C414
A415
C420
U421
A422
A423
U427
A428
A429
C433
U434
C435
C436
U441
G442
A443
C444
C445
G446
A447
U448
A449
G450
C453
A454
C455
C456
A457
G458
U459
A460
G465
A466
G467
G468
G469
A470
A471
A472
G473
G474
U475
G476
A477
A478
A479
A480
G481
A482
G489
G491
A492
G493
G494
G500
A501
A502
A503
U504
A505
G506
A507
G508
C509
C510
U511
G512
A513
A514
A515
C516
C517
G518
U525
A526
C527
A528
A529
G530
C531
A532
G533
A536
C537
G545
C546
A A548
G549
G553
U554
U555
G556
U557
G558
G559
C560
G563
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https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#residue_plots
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Page 21 Full wwPDB X-ray Structure Validation Report 4V8A
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Page 22 Full wwPDB X-ray Structure Validation Report 4V8A
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Page 23 Full wwPDB X-ray Structure Validation Report 4V8A
C A A2801A•
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• Molecule 1: 23S ribosomal RNA
Chain BA:
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Page 24 Full wwPDB X-ray Structure Validation Report 4V8A
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Page 25 Full wwPDB X-ray Structure Validation Report 4V8A
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G2837
G2838
G2839
G2845
G2846
U2847
G2848
U2849
G2852
C2853
G2854
C2863
G2864
U2865
U2866
C2871
G2872
A2873
C2874
C2875
C2880
C2881
A2882
A2883
U2884
C2889
G2891
A2892
G G2894
U2895
C2896
U2897
U G A C C C C U C C
• Molecule 2: 5S ribosomal RNA
Chain AB:
U1
C2
C3
C4
C5
C6
G7
U8
G9
C10
C11
C12
A13
U14
A15
G16
C17
G18
G19
C20
G21
U22
G23
G24
A25
A26
C27
C28
A29
C30
C31
C32
G33
C37
C38
A39
U40
C43
G44
A45
A46
C47
A48
C49
G50
G51•
A52•
A53
G54•
U55
G56
A57
A58
A59•
C60
G61
C62
G63
C64
C65
A66
G69
C70
C71
G72
A73
U74
G75
C79
U80
G87
C88
G89
A90
C91
C94
C95
U96
G97
G98
G99
G103
U104
A105
G106
G107
U108
C109
G110
G111
U112
G113
C114
G115
G116
G117
G118
G119
G120
U U
• Molecule 2: 5S ribosomal RNA
-
Page 26 Full wwPDB X-ray Structure Validation Report 4V8A
Chain BB:
U1
C2
C3
C4
C5
C6
G7
U8
G9
C12
A13
G16
G19
C20
G21
U22
G23
G24
A25
C28
A29
C30
C31
C32
G33
C36
C37
C38
A39
U40
C47
A48
C49
G50
G51
A52
A53
G54
U55
G56
C60
G61
A66
G69
A73
U74
G75
A78
C79
U80
C84
C88
G89
A90
C91
C92
G99
A100
G106
G107
U108
C109
G110
G111
U112
G116
G120
U U
• Molecule 3: 50S ribosomal protein L2
Chain AD:
MET
A2
V3
K4
K5
P8
Y9
T10
P11
S12
R13
R14
F15
M16
T17
K26
E30
K35
P36
R43
G47
R48
F53
R54
L61
K68
R69
W70
D71
I75
E83
S89
A93
L94
Y97
V98
D99
G100
E101
K102
R103
Y104
I105
I106
A107
P108
L111
I125
G128
N129
A130
L131
P132
L133
I136
V141
V142
H143
A144
V145
E148
P149
K150
K151
K154
L155
A156
A159
Y172
L175
P178
L182
V185
H186
Y190
A191
T192
V193
N198
A199
D200
V205
L206
G207
K208
R211
S212
R213
R217
R218
V221
R222
G223
A224
A225
M226
V229
D230
H231
P232
H233
G238
R239
R242
P246
Q253
L257
K258
T259
R260
R263
K264
P265
S266
S267
R274
K275
K276
• Molecule 3: 50S ribosomal protein L2
Chain BD:
MET
A2
V3
K4
K5
P8
Y9
S12
R13
R14
F15
M16
T17
K26
T27
E28
K31
K35
P36
Q46
G47
R48
I49
R54
R60
L61
I64
K68
R69
W70
D71
A77
K78
V79
E83
Y84
D85
R88
A93
L94
L95
H96
Y97
K102
R103
Y104
I105
I106
A107
P108
L111
Q112
V113
G128
L133
I136
P137
V138
V142
H143
A144
V145
E146
L147
E148
P149
K150
K151
G152
A153
K154
L155
A156
I165
Y172
V173
H186
C189
Y190
A191
T192
V193
K208
A209
G210
R211
S212
R213
V221
R222
G223
A224
A225
M226
V229
G238
R239
A240
P241
R242
G243
R244
P245
P246
A247
S248
P249
W250
Q253
T254
K255
G256
L257
K258
T259
R260
S267
R274
K275•
K276•
• Molecule 4: 50S ribosomal protein L3
Chain AE:
M1
K2
G3•
V7
K8
V9
G10
M11
T12
R13
I14
V21
P22
V23
T24
V25
I26
L27
A28
G29
P30
C31
P32
V33
V34
Q35
R36
R37
T38
D42
T45
A46
V47
Q48
L49
G50
F51
L52
P56
N60
R61
P62
L63
A68
K69
A70
G71
V72
E73
P74
V75
R76
I77
R82
D83
F84
N85
P86
E87
G88
V93
E94
I95
F96
R101
V104
T105
G106
T107
S108
K109
G110
R111
G112
F113
A114
G115
V116
M117
K118
R119
W120
N121
F122
S128
H129
R136
H137
I141
G142
N143
R144
P147
G148
R149
V150
Y151
K152
G153
K154
K155
M156
H159
Y160
E163
R164
V165
M168
N169
L170
E171
V172
V175
I176
L181
L182
L183
V184
A187
V188
P189
G190
L195
R199
E200
T201
K202
K203
A204
ALA
LYS
• Molecule 4: 50S ribosomal protein L3
-
Page 27 Full wwPDB X-ray Structure Validation Report 4V8A
Chain BE:
M1
K2
G6
V9
G10
M11
T12
R13
I14
V21
T24
V25
A28
G29
P30
C31
P32
V33
R36
T45
A46
V47
Q48
L49
G50
F51
L52
P53
Q54
P62
K69
A70
G71
V72
E73
P74
V75
R76
I77
R82
D83
F84
N85
P86
E87
T92
V93
R101
T105
G110
R111
G115
V116
M117
K118
R119
W120
N121
F122
D127
S128
H129
K133
I134
H135
N143
R144
K145
T146
P147
G148
R149
K152
G153
K154
K155
Y160
G161
A162
E163
M168
N169
L170
D174
V175
E179
N180
L181
V184
K185
G186
L195
R199
E200
T201
K202
K203
A204
ALA
LYS
• Molecule 5: 50S ribosomal protein L4
Chain AF:
V6
Y7
P10
V11
L12
S13
R17
R18
E19
L20
A21
A22
D23
L24
I28
L33
W34
E35
R38
W39
K43
S50
T53
R54
G55
E56•
S60
G61
I64
R74
D77
I78
G79
A80
P81
I82
F83
V88
V89
F90
G91
D96
Y97
S98
L101
P102
K103
R106
K107
K108
G109
L110
A113
D116
R117
A118
R119
E120
L123
L124
L125
F129
V132
K135
T136
K137
E138
F139
L140
A141
W142
A143
L148
L155
L156
V157
T158
G159
N160
E161
L162
V163
A166•
A167
R168
N169
L170
P171
W172
V173
V174
T175
L176
E179
G180
L181
N182
V183
Y184
D185
I186
V187
R188
L192
V193
M194
D197
A198
W199
E200
V201
R205
G208
GLU
ALA
• Molecule 5: 50S ribosomal protein L4
Chain BF:
V6
Y7
S15
R18
A22
D23
L24
I28
N29
L32
L33
V37
R38
W39
Q40
L41
R45
S50
T53
R54
G55
Y59
R62
K63
I64
W65
P66
R74
H75
G76
P81
I82
F83
V89
F90
R95
L101
P102
K103
K104
V105
R106
K107
K108
G109
L110
A111
M112
A113
V114
A115
D116
R117
L123
L124
F129
A130
G131
V132
L140
D149
G150
V154
V157
T158
G159
N160
E161
L162
V163
R168
W172
V173
V174
T175
L176
G180
L181
N182
V183
Y184
D185
I186
V187
R188
L192
V193
M194
D197
A198
W199
E200
V201
F202
R205
I206
G207
G208
GLU
ALA
• Molecule 6: 50S ribosomal protein L5
Chain AG:
MET
P2•
L3•
D4
V5
A6
L7
K8•
R9•
K10
Y11•
Y12•
E13•
E14
V15
R16•
P17•
E18
L19
I20
R21
Y25
Q26•
N27
V28•
W29•
E30
V31
P32
R33
L34•
E35•
K36
I39•
N40
Q41•
G42
L43•
G44•
E45
A46
D49•
A50
R51
I52
A56
L60
A61
L62•
I63
T64
G65•
Q66
T71
R72•
K75•
S76
I77
S78
N79
F80•
R83
K84
G85•
M86
P87•
I88
G89
L90•
R91
L94
R95
R96
D97
R98
M99
W100•
I101•
F102
L103
E104
K105
L106
L107•
N108•
V109
A110
L111
P112
R113
I114
R115
D116
F117•
L120•
N121
P122
N123
S124
F125
D126
G127
R128
G129
N130
Y131•
N132•
L133•
G134•
L135•
-
Page 28 Full wwPDB X-ray Structure Validation Report 4V8A
Q138•
L139
I140
F141
P142•
E143
I144
T145•
Y146
D147
M148•
V149
D150
A151•
L152
R153
G154
M155•
D156•
I157•
A158
V159•
V160•
T161•
R170
A171•
L172•
L173
E174
L175
L176•
G177
F178
P179
F180
R181
K182
• Molecule 6: 50S ribosomal protein L5
Chain BG:
MET
P2
V5
A6
L7
K8
R9
K10
Y11
Y12
E13
E14
V15
R16
L19
I20
R21
G24
Y25
Q26
N27
V28
W29
E30
V31
L34
I39
N40
Q41
G42
L43
G44
E45
A46
K47
E48
D49•
A50
R51
I52
L53
E54
K55
A56
L60
A61
Q66
K67
P68
T71
R72
A73•
K74
K75•
S76
I77
S78
N79
F80•
K81
L82
R83
M86
P87•
I88•
G89
L90
R91
R96
M99
F102
L103
E104
K105
L106
L107
N108
V109
A110
L111
P112
R113
I114
R115
D116
F117
N121
P122
N123
S124
F125
D126
N130
Y131
N132
L133
G134
E137
Q138
L139
E143
I144
T145•
Y146•
D147
M148
V149
D150
A151
L152
R153
I157
A158
V159
V160
T161
T165
E168
A169
R170
L175
L176
G177
F178
P179
F180
R181
K182
• Molecule 7: 50S ribosomal protein L6
Chain AH:
MET
S2
R3
I4
G5
R6
L7
P8
I9
P10
V11
P12
K13•
G14
V15
S16
V17
E18•
G22
R23
V24•
K25
V26
K27•
G28
P29•
K30•
G31
E32•
L33
E34•
V35
P36
V37
E40
M41•
R42
V43•
V44
V45
E46•
E47•
V50
R51
V52•
E53
R54
P55
S56•
D57
R60
H61
K62
S63
L64
H65
G66
L67
T68
R69
T70
L71
I72
A73
V76
S80
Y83
E86
L87
L88•
I89•
K90•
G91
I92
G93
Y94•
R95
A96•
R97•
L98
V99•
G100•
R101•
A102
L105•
T106•
V107
G108
H111•
P112•
V113
E116
P117
P118
I121
E124
V125
P126
E127
P128•
V131
R132
I136
D137
K138
Q139
K140
Q143
V144
A145
I148•
R149
A150
I151
R152
K153
P154
S155
A156•
Y157•
H158•
E159•
I162
Y163
Y164
A165
G166•
E167
P168
V169•
R170
L171•
K175•
ALA
GLY
ALA
LYS
LYS
• Molecule 7: 50S ribosomal protein L6
Chain BH:
MET
S2
R3
I4
G5
R6
L7
P8
V11
P12
V15
S16
V17
A20
P21
G22
R23
V24
K25
V26
K27
E32
L33
E40
M41
R42
V43
V44
V45
V50
R51
V52
R60
H61
K62
R69
T70
L71
I72
Y83
L88
I89
K90
G91
I92
L98
L105
T106
V107
G108
F109
S110
T122
F123
E124
V125
P126
E127
R132
I136
D137
K138
Q139
K140
V144
I148
R149
P154
H158
E159
K160
Y163
Y164
A165
G166
E167
P168
V169
R170
L171
K175
ALA
GLY
ALA
LYS
LYS
• Molecule 8: 50S ribosomal protein L9
Chain AI:
M1
K2
V3•
I4•
L5
L9
E10
N11
L12
V15
V19
K22
Y25
A26
R27•
N28
Y29
P32
L38
L44
K45
A46
L47
E48
I51
Q54
R57
R61
K62
A63
E66
R67
L68•
L72
E73
N74
L75
T76
L77
T78
I79•
P80
V81•
R82•
A83
G84•
-
Page 29 Full wwPDB X-ray Structure Validation Report 4V8A
E85•
T86•
K87•
I88
Y89•
G90
S91
V92
T93•
A94
K95
D96
I97
A98
E99
A100•
L101
S102
R103
Q104
H105
G106
V107
T108•
I109
E110
P111
K112
ARG
L114
A115
L116
E117•
K118
P119•
I120
K121•
E122•
L123
G124
E125
Y126
V127
L128
T129
P132
H133
P134
E135
V136
P137
I138
Q139
L140
K141
V142
S143
V144
V145•
A146•
GLN
GLU
• Molecule 8: 50S ribosomal protein L9
Chain BI:
M1
K2
V3
I4
L5
L9
E10
N11
L12•
V15
V19
D20
V21
G24
Y25
A26
R27
N28
Y29
L30
L31
P32
L35
L38
A39
T40
E41
S42
N43
L44
L47
R57
E60
R61
K62
A65
E66
L72
L75
T76
L77
T78
I79
P80
V81
R82
A83
G84
E85
T86
Y89
V92
T93
A94
I97
L101
Q104
H105
G106
V107
T108
I109
E110
P111
K112
ARG
L114
A115
L116
E117
K118
P119
I120
K121
E122
L123
Y130
H133
V136
P137
I138
Q139
L140
K141
V142
S143
V144
V145
A146
GLN
GLU
• Molecule 9: 50S ribosomal protein L13
Chain AN:
M1
K2
T3
Y4
V5
V9
R12
L15
I16
D17
A18
E19
G20
L23
G24
R25
L26
A27
T28
K29
I30
L33
L34
K37
H38
W42
T43
P44•
N45
V46
A47
M48
G49
D50
F51
V52
V55
N56
A57
D58
K59
I60
R61
V62
T63
G64
K65
K66
K70
I71
Y72
T73
R74
Y75
S76
G77
K83
K84
I85
P86
L87
T93
H94
P95
E96
R97
V98
L99
E100
V103
K104
G105
M106
L107
P111
L112
G113
R114
R115
L120
K121
V122
Y123
A124
G125
P126
D127
H128
P129
H130
Q131
A132
Q133
R134
P135
L138
E139
V140
• Molecule 9: 50S ribosomal protein L13
Chain BN:
M1
K2
V5
V9
R12
W13
V14
L15
A18
E19
G20
K21
T22
L23
G24
R25
L26
A27
T28
K29
L33
L34
R35
G36
K37
H38
R39
P40
D41
W42
T43
P44
N45
V46
A47
M48
V55
N56
K59
I60
R61
V62
T63
G64
L67
T73
R74
Y75
S76
G77
G81
L87
E88
K89
T93
E96
R97
V98
L99
K104
P108
L112
G113
R114
R115
L116
F117
L120
K121
G125
P126
D127
H128
Q131
A132
Q133
R134
P135
E136
K137
L138
E139
V140
• Molecule 10: 50S ribosomal protein L14
Chain AO:
M1
I2
Q3
P4
Q5
T6
Y7
L8
E9
V10
T14
G15
A16
R17
M20
R23
V24
L25
K26
G27
S28
N29
V35
G36
D37
V43
K44
I47
P48
V52
K53
D56
R64
T65
K66
K67
K70
D73
G74
S75
A76
I77
D80
D81
N82
A83
R94
V98
V102
A103
R104
E105
L106
K113
I114
V115
A118
P119
E120
V121
L122
• Molecule 10: 50S ribosomal protein L14
-
Page 30 Full wwPDB X-ray Structure Validation Report 4V8A
Chain BO:
M1
I2
Q5
T6
Y7
L8
E9
V10
A16
R17
K18
I19
R23
V24
L25
K26
G27
S28
N29
A33
T34
V35
S42
I47
P48
V52
K53
V63
K67
E68
I69
K70
R78
F79
D80
N88
R94
V98
V102
A103
R104
E105
L106
R107
M112
K113
I114
V115
E120
V121
L122
• Molecule 11: 50S ribosomal protein L15
Chain AP:
M1
K2
L3
L6
R18
R21
G26
H27
G28
K29
R33
G37
Q38
K39
S40
R41
S42
G43
GLY
LEU
K46
R50
F51
E52
R55
S56
T57
T58
L59
P63
K64
R65
G66•
K76
Y80
Q81
G82
V83
N84
L85
K86
D87
L88
E92•
G93•
L100
V101
R102
A103
L106
L112
K113
I114
E117
G118
E119
A120
K121
P122•
L123
H128
A129
K132
S133
A134
L135
L138
K139
A140
G143
E144
P145
V146
L147
L148
E149
ALA
• Molecule 11: 50S ribosomal protein L15
Chain BP:
M1
K2
L3
L6
V19
G20
R21
G26
H27
G28
K29
T30
A31
T32
R33
Q38
K39
S40
R41
S42
G43
GLY
LEU
K46
R50
F51
E52
R55
L59
M60
R61
R65
G66
Q70
E74
I75
K76
R77
G82
V83
R90
F91
V95
E98
L99
L100
V101
R102
A103
L106
K107
K108
L112
K113
G116
E117
G118
E119
A120
K121
P122
L123
V126
K132
L135
E144
L148
E149
ALA
• Molecule 12: 50S ribosomal protein L16
Cha