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- PDB-6aoc: Crystal Structure of an N-Hydroxythienopyrimidine-2,4-dione RNase... -

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Basic information

Entry
Database: PDB / ID: 6aoc
TitleCrystal Structure of an N-Hydroxythienopyrimidine-2,4-dione RNase H Active Site Inhibitor with Multiple Binding Modes to HIV Reverse Transcriptase
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE / TRANSFERASE INHIBITOR / HIV-1 / TRANSFERASE - TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / TRIETHYLENE GLYCOL / Chem-ZW2 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKirby, K.A. / Sarafianos, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100890 United States
CitationJournal: Eur J Med Chem / Year: 2017
Title: Design, synthesis and biological evaluations of N-Hydroxy thienopyrimidine-2,4-diones as inhibitors of HIV reverse transcriptase-associated RNase H.
Authors: Kankanala, J. / Kirby, K.A. / Huber, A.D. / Casey, M.C. / Wilson, D.J. / Sarafianos, S.G. / Wang, Z.
History
DepositionAug 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reverse transcriptase/ribonuclease H
B: p51 RT
C: Reverse transcriptase/ribonuclease H
D: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,44485
Polymers228,4044
Non-polymers6,04081
Water20,6631147
1
A: Reverse transcriptase/ribonuclease H
B: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,38543
Polymers114,2022
Non-polymers3,18341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint46 kcal/mol
Surface area47030 Å2
MethodPISA
2
C: Reverse transcriptase/ribonuclease H
D: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,05942
Polymers114,2022
Non-polymers2,85740
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13950 Å2
ΔGint84 kcal/mol
Surface area47420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.370, 89.120, 112.730
Angle α, β, γ (deg.)105.720, 95.030, 110.720
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 21 or resid 23...
21(chain C and (resid 1 through 21 or resid 23...
12(chain B and (resid 4 through 21 or resid 23...
22(chain D and (resid 4 through 21 or resid 23...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 21 or resid 23...A1 - 21
121(chain A and (resid 1 through 21 or resid 23...A23 - 39
131(chain A and (resid 1 through 21 or resid 23...A41 - 42
141(chain A and (resid 1 through 21 or resid 23...A44 - 52
151(chain A and (resid 1 through 21 or resid 23...A54 - 59
161(chain A and (resid 1 through 21 or resid 23...A61 - 71
171(chain A and (resid 1 through 21 or resid 23...A73 - 81
181(chain A and (resid 1 through 21 or resid 23...A83 - 103
191(chain A and (resid 1 through 21 or resid 23...A105 - 133
1101(chain A and (resid 1 through 21 or resid 23...A136 - 160
1111(chain A and (resid 1 through 21 or resid 23...A162 - 163
1121(chain A and (resid 1 through 21 or resid 23...A165 - 168
1131(chain A and (resid 1 through 21 or resid 23...A170 - 1781
1141(chain A and (resid 1 through 21 or resid 23...A183 - 198
1151(chain A and (resid 1 through 21 or resid 23...A200198
1161(chain A and (resid 1 through 21 or resid 23...A200 - 211
1171(chain A and (resid 1 through 21 or resid 23...A213 - 296
1181(chain A and (resid 1 through 21 or resid 23...A304
1191(chain A and (resid 1 through 21 or resid 23...A312
1201(chain A and (resid 1 through 21 or resid 23...A308 - 321
1211(chain A and (resid 1 through 21 or resid 23...A363
1221(chain A and (resid 1 through 21 or resid 23...A363
1231(chain A and (resid 1 through 21 or resid 23...A365 - 366
1241(chain A and (resid 1 through 21 or resid 23...A374 - 385
1251(chain A and (resid 1 through 21 or resid 23...A393 - 394
1261(chain A and (resid 1 through 21 or resid 23...A403 - 398
1271(chain A and (resid 1 through 21 or resid 23...A406 - 4006
1281(chain A and (resid 1 through 21 or resid 23...A414 - 416
1291(chain A and (resid 1 through 21 or resid 23...A424416
1301(chain A and (resid 1 through 21 or resid 23...A424 - 427
1311(chain A and (resid 1 through 21 or resid 23...A429 - 447
1321(chain A and (resid 1 through 21 or resid 23...A450 - 460
1331(chain A and (resid 1 through 21 or resid 23...A462 - 466
1341(chain A and (resid 1 through 21 or resid 23...A468 - 4706
1351(chain A and (resid 1 through 21 or resid 23...A508
1361(chain A and (resid 1 through 21 or resid 23...A510 - 511
1371(chain A and (resid 1 through 21 or resid 23...A513 - 519
1381(chain A and (resid 1 through 21 or resid 23...A521 - 522
1391(chain A and (resid 1 through 21 or resid 23...A524 - 539
1401(chain A and (resid 1 through 21 or resid 23...A541 - 542
1411(chain A and (resid 1 through 21 or resid 23...A545 - 546
1421(chain A and (resid 1 through 21 or resid 23...A548 - 555
211(chain C and (resid 1 through 21 or resid 23...C1 - 21
221(chain C and (resid 1 through 21 or resid 23...C23 - 39
231(chain C and (resid 1 through 21 or resid 23...C41 - 42
241(chain C and (resid 1 through 21 or resid 23...C-1 - 59
251(chain C and (resid 1 through 21 or resid 23...C61 - 71
261(chain C and (resid 1 through 21 or resid 23...C73 - 81
271(chain C and (resid 1 through 21 or resid 23...C-1 - 562
281(chain C and (resid 1 through 21 or resid 23...C105 - 133
291(chain C and (resid 1 through 21 or resid 23...C162 - 163
2101(chain C and (resid 1 through 21 or resid 23...C173 - 181
2111(chain C and (resid 1 through 21 or resid 23...C173 - 181
2121(chain C and (resid 1 through 21 or resid 23...C183 - 198
2131(chain C and (resid 1 through 21 or resid 23...C200 - 211
2141(chain C and (resid 1 through 21 or resid 23...C304 - 306
2151(chain C and (resid 1 through 21 or resid 23...C312
2161(chain C and (resid 1 through 21 or resid 23...C329 - 352
2171(chain C and (resid 1 through 21 or resid 23...C360 - 355
2181(chain C and (resid 1 through 21 or resid 23...C360 - 355
2191(chain C and (resid 1 through 21 or resid 23...C363
2201(chain C and (resid 1 through 21 or resid 23...C374 - 385
2211(chain C and (resid 1 through 21 or resid 23...C393 - 394
2221(chain C and (resid 1 through 21 or resid 23...C403 - 398
2231(chain C and (resid 1 through 21 or resid 23...C403 - 398
2241(chain C and (resid 1 through 21 or resid 23...C414 - 416
2251(chain C and (resid 1 through 21 or resid 23...C424 - 426
2261(chain C and (resid 1 through 21 or resid 23...C450 - 467
2271(chain C and (resid 1 through 21 or resid 23...C429 - 447
2281(chain C and (resid 1 through 21 or resid 23...C462 - 460
2291(chain C and (resid 1 through 21 or resid 23...C468 - 476
2301(chain C and (resid 1 through 21 or resid 23...C477 - 505
2311(chain C and (resid 1 through 21 or resid 23...C508
2321(chain C and (resid 1 through 21 or resid 23...C513 - 519
2331(chain C and (resid 1 through 21 or resid 23...C521 - 522
2341(chain C and (resid 1 through 21 or resid 23...C521 - 522
2351(chain C and (resid 1 through 21 or resid 23...C545 - 542
2361(chain C and (resid 1 through 21 or resid 23...C545 - 546
2371(chain C and (resid 1 through 21 or resid 23...C548 - 555
112(chain B and (resid 4 through 21 or resid 23...B4 - 21
122(chain B and (resid 4 through 21 or resid 23...B23 - 27
132(chain B and (resid 4 through 21 or resid 23...B29
142(chain B and (resid 4 through 21 or resid 23...B31
152(chain B and (resid 4 through 21 or resid 23...B33 - 42
162(chain B and (resid 4 through 21 or resid 23...B0
172(chain B and (resid 4 through 21 or resid 23...B66
182(chain B and (resid 4 through 21 or resid 23...B0 - 72
192(chain B and (resid 4 through 21 or resid 23...B74 - 92
1102(chain B and (resid 4 through 21 or resid 23...B95 - 101
1112(chain B and (resid 4 through 21 or resid 23...B0 - 428
1122(chain B and (resid 4 through 21 or resid 23...B3 - 12225
1132(chain B and (resid 4 through 21 or resid 23...B0 - 428
1142(chain B and (resid 4 through 21 or resid 23...B127 - 139
1152(chain B and (resid 4 through 21 or resid 23...B0
1162(chain B and (resid 4 through 21 or resid 23...B170 - 171
1172(chain B and (resid 4 through 21 or resid 23...B173
1182(chain B and (resid 4 through 21 or resid 23...B175 - 183
1192(chain B and (resid 4 through 21 or resid 23...B185 - 196
1202(chain B and (resid 4 through 21 or resid 23...B207 - 214
1212(chain B and (resid 4 through 21 or resid 23...B226 - 22
1222(chain B and (resid 4 through 21 or resid 23...B235
1232(chain B and (resid 4 through 21 or resid 23...B243
1242(chain B and (resid 4 through 21 or resid 23...B245 - 240
1252(chain B and (resid 4 through 21 or resid 23...B248 - 245
1262(chain B and (resid 4 through 21 or resid 23...B287 - 282
1272(chain B and (resid 4 through 21 or resid 23...B290 - 30
1282(chain B and (resid 4 through 21 or resid 23...B315 - 310
1292(chain B and (resid 4 through 21 or resid 23...B318
1302(chain B and (resid 4 through 21 or resid 23...B326 - 321
1312(chain B and (resid 4 through 21 or resid 23...B329 - 331
1322(chain B and (resid 4 through 21 or resid 23...B339
1332(chain B and (resid 4 through 21 or resid 23...B347 - 351
1342(chain B and (resid 4 through 21 or resid 23...B359 - 374
1352(chain B and (resid 4 through 21 or resid 23...B382 - 383
1362(chain B and (resid 4 through 21 or resid 23...B391 - 389
1372(chain B and (resid 4 through 21 or resid 23...B397 - 402
1382(chain B and (resid 4 through 21 or resid 23...B410 - 408
1392(chain B and (resid 4 through 21 or resid 23...B416 - 414
1402(chain B and (resid 4 through 21 or resid 23...B422 - 424
212(chain D and (resid 4 through 21 or resid 23...D4 - 21
222(chain D and (resid 4 through 21 or resid 23...D23 - 27
232(chain D and (resid 4 through 21 or resid 23...D29
242(chain D and (resid 4 through 21 or resid 23...D3
252(chain D and (resid 4 through 21 or resid 23...D33 - 44
262(chain D and (resid 4 through 21 or resid 23...D44 - 54
272(chain D and (resid 4 through 21 or resid 23...D5
282(chain D and (resid 4 through 21 or resid 23...D4 - 428
292(chain D and (resid 4 through 21 or resid 23...D4 - 428
2102(chain D and (resid 4 through 21 or resid 23...D95 - 101
2112(chain D and (resid 4 through 21 or resid 23...D4 - 428
2122(chain D and (resid 4 through 21 or resid 23...D127 - 139
2132(chain D and (resid 4 through 21 or resid 23...D167 - 168
2142(chain D and (resid 4 through 21 or resid 23...D167 - 168
2152(chain D and (resid 4 through 21 or resid 23...D170 - 171
2162(chain D and (resid 4 through 21 or resid 23...D173
2172(chain D and (resid 4 through 21 or resid 23...D185 - 196
2182(chain D and (resid 4 through 21 or resid 23...D198 - 205
2192(chain D and (resid 4 through 21 or resid 23...D207 - 225
2202(chain D and (resid 4 through 21 or resid 23...D207 - 225
2212(chain D and (resid 4 through 21 or resid 23...D246 - 243
2222(chain D and (resid 4 through 21 or resid 23...D246 - 243
2232(chain D and (resid 4 through 21 or resid 23...D285 - 280
2242(chain D and (resid 4 through 21 or resid 23...D313 - 305
2252(chain D and (resid 4 through 21 or resid 23...D324 - 318
2262(chain D and (resid 4 through 21 or resid 23...D316
2272(chain D and (resid 4 through 21 or resid 23...D327 - 329
2282(chain D and (resid 4 through 21 or resid 23...D337 - 339
2292(chain D and (resid 4 through 21 or resid 23...D345 - 347
2302(chain D and (resid 4 through 21 or resid 23...D357 - 379
2312(chain D and (resid 4 through 21 or resid 23...D380 - 382
2322(chain D and (resid 4 through 21 or resid 23...D389 - 381
2332(chain D and (resid 4 through 21 or resid 23...D395 - 407
2342(chain D and (resid 4 through 21 or resid 23...D408 - 400
2352(chain D and (resid 4 through 21 or resid 23...D414 - 416
2362(chain D and (resid 4 through 21 or resid 23...D414 - 412
2372(chain D and (resid 4 through 21 or resid 23...D420 - 422

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Reverse transcriptase/ribonuclease H


Mass: 64105.441 Da / Num. of mol.: 2 / Fragment: p66 domain residues 168-722 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Plasmid: pET35a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) RIL
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein p51 RT / Exoribonuclease H / p66 RT


Mass: 50096.539 Da / Num. of mol.: 2 / Fragment: p51 domain residues 168-595 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Plasmid: pET35a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) RIL / References: UniProt: P03366

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Non-polymers , 5 types, 1228 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-ZW2 / 6-benzyl-3-hydroxythieno[2,3-d]pyrimidine-2,4(1H,3H)-dione


Mass: 274.295 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10N2O3S
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 68 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1147 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.92 % / Mosaicity: 0.139 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: PEG 3350, SODIUM POTASSIUM PHOSPHATE, ETHYLENE GLYCOL, TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.8→55.32 Å / Num. obs: 217194 / % possible obs: 97.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 36.81 Å2 / Rpim(I) all: 0.033 / Rrim(I) all: 0.062 / Net I/σ(I): 9.9 / Num. measured all: 761476
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.8-1.833.20.734281105750.9841.81294.6
4.88-55.343.529.938373110060.020.03898.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
xia20.4.0.338data scaling
XDSdata reduction
PDB_EXTRACT3.22data extraction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KFB

4kfb


Resolution: 1.8→55.318 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2258 10774 4.96 %
Rwork0.1863 206361 -
obs0.1883 217135 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 196.69 Å2 / Biso mean: 61.5361 Å2 / Biso min: 22.92 Å2
Refinement stepCycle: final / Resolution: 1.8→55.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15992 0 384 1147 17523
Biso mean--73.09 60.52 -
Num. residues----1950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117540
X-RAY DIFFRACTIONf_angle_d0.98323765
X-RAY DIFFRACTIONf_chiral_restr0.062533
X-RAY DIFFRACTIONf_plane_restr0.0082996
X-RAY DIFFRACTIONf_dihedral_angle_d18.94410781
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5967X-RAY DIFFRACTION9.484TORSIONAL
12C5967X-RAY DIFFRACTION9.484TORSIONAL
21B4441X-RAY DIFFRACTION9.484TORSIONAL
22D4441X-RAY DIFFRACTION9.484TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82050.38373380.37956607694593
1.8205-1.84190.37853750.35236812718796
1.8419-1.86430.37723520.32836751710396
1.8643-1.88790.37123650.31076789715496
1.8879-1.91280.34393420.29566808715096
1.9128-1.9390.28173730.27836836720996
1.939-1.96670.32513550.27226806716196
1.9667-1.99610.30663480.2716870721896
1.9961-2.02720.30683830.26026816719996
2.0272-2.06050.28153520.24876870722297
2.0605-2.0960.27343860.23466760714696
2.096-2.13410.25363240.22466911723597
2.1341-2.17520.25383400.21586889722997
2.1752-2.21960.24943370.20776854719197
2.2196-2.26780.25713250.20376948727397
2.2678-2.32060.23453510.19936875722697
2.3206-2.37860.223430.20126906724997
2.3786-2.44290.2493500.20286920727097
2.4429-2.51480.23913910.19296909730098
2.5148-2.5960.23573780.19156890726898
2.596-2.68880.23623730.19166929730298
2.6888-2.79640.21933310.19136978730998
2.7964-2.92370.22483450.19046976732198
2.9237-3.07780.24343590.19586953731298
3.0778-3.27060.243980.18466927732598
3.2706-3.52310.22393580.17687018737698
3.5231-3.87760.21913590.16076938729798
3.8776-4.43850.18143800.13986936731698
4.4385-5.59120.16483620.14276964732698
5.5912-55.34390.21924010.18686915731698
Refinement TLS params.Method: refined / Origin x: -12.6082 Å / Origin y: 29.8951 Å / Origin z: -11.1644 Å
111213212223313233
T0.2257 Å2-0.0231 Å20.0286 Å2-0.3088 Å2-0.0115 Å2--0.3325 Å2
L0.0302 °2-0.1207 °20.2069 °2-0.2402 °2-0.1516 °2--0.3924 °2
S-0.0046 Å °0.0361 Å °0.0006 Å °0.0018 Å °-0.005 Å °-0.0824 Å °-0.0477 Å °0.0284 Å °0.0195 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 562
2X-RAY DIFFRACTION1allB0 - 428
3X-RAY DIFFRACTION1allC-1 - 562
4X-RAY DIFFRACTION1allD4 - 428
5X-RAY DIFFRACTION1allL1 - 11
6X-RAY DIFFRACTION1allW1 - 1483
7X-RAY DIFFRACTION1allI1 - 90

+
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