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- PDB-3zfg: Human enterovirus 71 in complex with capsid binding inhibitor WIN51711 -

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Basic information

Entry
Database: PDB / ID: 3zfg
TitleHuman enterovirus 71 in complex with capsid binding inhibitor WIN51711
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / EV71 / INHIBITOR / PICORNAVIRUS
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A ...Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Few Secondary Structures / Irregular / Viral coat protein subunit / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-W71 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHUMAN ENTEROVIRUS 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPlevka, P. / Perera, R. / Yap, M.L. / Cardosa, J. / Kuhn, R.J. / Rossmann, M.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure of Human Enterovirus 71 in Complex with a Capsid-Binding Inhibitor.
Authors: Plevka, P. / Perera, R. / Yap, M.L. / Cardosa, J. / Kuhn, R.J. / Rossmann, M.G.
History
DepositionDec 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Oct 24, 2018Group: Data collection / Refinement description / Category: struct_ncs_oper
Item: _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] ..._struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3]
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0015
Polymers94,6594
Non-polymers3421
Water00
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,700,057300
Polymers5,679,511240
Non-polymers20,54660
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 475 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)475,00525
Polymers473,29320
Non-polymers1,7125
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 570 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)570,00630
Polymers567,95124
Non-polymers2,0556
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
Unit cell
Length a, b, c (Å)592.500, 592.500, 592.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), ()1
2generate(0.56443163, -0.76531488, -0.30937047), (312.21477, 0.74410918, 0.30945715), (0.59206233, -272.9304, -0.35737721)-0.56438411, 0.74414522, 247.88406
3generate(-0.14033281, -0.4941963, -0.85794914), (620.62835, 0.43867907, -0.80786467), (0.39359287, 21.69402, -0.88761894)-0.32113034, 0.33016349, 474.80493
4generate(-0.14033281, 0.43867907, -0.88761894), (499.02365, -0.49419629, -0.80786467), (-0.32113034, 476.71233, -0.85794914)0.39359287, 0.33016349, 367.16569
5generate(0.56443163, 0.74410918, -0.35737721), (115.45424, -0.76531487, 0.30945714), (-0.56438411, 463.30469, -0.30937046)0.59206234, 0.74414522, 73.7201
6generate(-0.97893114, -0.01909326, -0.20329601), (379.97061, -0.01909326, -0.9826971), (0.18423317, 206.94088, -0.20329601)0.18423318, 0.96162824, 19.94319
7generate(-0.4940938, 0.85801906, 0.14026624), (29.15114, -0.8078515, -0.39346856), (-0.43881481, 514.85607, -0.32132112)-0.33012996, 0.88756236, 144.56065
8generate(0.30944973, 0.56449343, 0.76523724), (-324.52196, -0.59193809, 0.74415922), (-0.30957446, 261.24723, -0.7442111)-0.35717534, 0.56442504, 354.35451
9generate(0.3212296, -0.49402769, 0.80792832), (-192.2845, 0.33026199, 0.85802332), (0.39334845, -203.40683, -0.88754637)0.14047284, 0.43878107, 359.3968
10generate(-0.47503356, -0.8547041, 0.20934186), (243.11586, 0.68429956, -0.20923258), (0.69853835, -236.97, -0.55324247)0.4750817, 0.68426614, 152.71923
11generate(0.96168803, 0.20301066, 0.18423575), (-106.33463, 0.20301065, -0.97899089), (0.01906614, 248.26706, 0.18423576)0.01906614, -0.98269714, 858.65262
12generate(0.62802757, -0.77715078, -0.04022476), (184.1799, -0.62070427, -0.46908343), (-0.62824115, 583.57255, 0.46936934)0.41952044, -0.77697813, 667.37506
13generate(-0.20943099, -0.69843149, -0.68434795), (582.39638, -0.47487533, 0.68444232), (-0.5532017, 362.07567, 0.85477019)0.20912237, -0.47501132, 506.81873
14generate(-0.39334839, 0.33038115, -0.85797747), (537.99317, 0.43896683, 0.88745297), (0.14048252, -110.12242, 0.80782743)-0.32136508, -0.49410458, 598.86701
15generate(0.33044296, 0.88750303, -0.32116322), (112.334, 0.85792342, -0.14060528), (0.4941635, -180.46001, 0.39341436)-0.43882629, -0.80787167, 816.31232
16generate(-0.98275689, -0.1839174, 0.01906026), (304.76401, -0.1839174, 0.96168798), (-0.20329931, 123.19214, 0.01906026)-0.20329932, -0.9789311, 913.00424
17generate(-0.6983654, 0.6844466, 0.20932899), (52.85418, 0.6844466, 0.55309484), (0.47499363, -247.09814, 0.20932899)0.47499363, -0.85472944, 731.78028
18generate(0.04031407, 0.62813436, 0.77705985), (-300.10277, 0.62813435, -0.62073687), (0.4691833, -66.61685, 0.77705985)0.4691833, -0.4195772, 455.62188
19generate(0.2124516, -0.27503252, 0.93766808), (-266.33234, -0.27503253, -0.93761162), (-0.21270063, 415.217, 0.93766808)-0.21270063, -0.27483998, 466.17056
20generate(-0.41984103, -0.77690811, 0.46919857), (107.49589, -0.77690811, 0.04038072), (-0.62831774, 532.5254, 0.46919857)-0.62831774, -0.6205397, 748.8484
21generate(0.20313837, -0.97896101, 0.01923897), (248.16683, -0.18425095, -0.01892042), (0.98269711, -266.17145, -0.96165814)-0.2031683, -0.18421796, 698.84514
22generate(-0.62067172, -0.46926947, -0.62813437), (583.54689, -0.46926947, -0.4194637), (0.77706909, -74.93841, -0.62813436)0.77706909, 0.04013542, 408.38738
23generate(-0.47503356, 0.68429956, -0.55324246), (362.13742, -0.8547041, -0.20923258), (0.4750817, 85.65616, 0.20934185)0.69853836, 0.68426614, 10.13771
24generate(0.43878587, 0.88755289, 0.14041662), (-110.08121, -0.80789728, 0.32124068), (0.49407126, -6.32397, 0.39340684)-0.33023368, 0.85800744, 54.46364
25generate(0.85791917, -0.14039868, 0.4942296), (-180.51891, -0.39353445, 0.43886007), (0.80779483, -223.76539, -0.33031096)-0.88751905, 0.32125475, 480.10824
26generate(-0.18407813, 0.96168803, -0.20315357), (123.15007, -0.01904817, 0.2031564), (0.978961, -320.49868, 0.98272702)0.18407502, -0.01907827, 287.72559
27generate(0.68430383, 0.55313561, 0.47515184), (-247.15427, -0.2094392, -0.47506399), (0.85466334, -139.22453, 0.69847226)-0.68436481, -0.20923984, 539.57862
28generate(0.62802757, -0.62070427, 0.46936933), (-66.68947, -0.77715078, -0.46908342), (0.41952045, 136.90228, -0.04022475)-0.62824115, -0.77697814, 892.56871
29generate(-0.27513503, -0.93762481, -0.21250986), (415.14825, -0.93762481, 0.21283316), (0.27488501, 126.28388, -0.21250985)0.274885, -0.93769814, 858.87557
30generate(-0.77704395, 0.04034742, -0.62815187), (532.47554, -0.46909162, 0.62830022), (0.62063829, -156.40546, 0.41970912)0.77692401, -0.46929026, 485.06196
31generate(0.00016073, 0.99999998, -0.00014574), (0.04202, 1.497E-5, -0.00014575), (-0.99999999, 592.51894, -0.99999999)0.00016073, -1.498E-5, 592.48348
32generate(0.74425197, 0.30941638, 0.59190414), (-272.87432, 0.3572772, 0.56432754), (-0.74423613, 344.67934, -0.56430666)0.76537306, 0.30945448, 280.22113
33generate(0.43878587, -0.80789728, 0.39340684), (21.7666, 0.88755289, 0.32124068), (-0.33023369, 117.72014, 0.14041661)0.49407125, 0.85800744, -28.14849
34generate(-0.4940938, -0.80785151, -0.32132112), (476.78104, 0.85801905, -0.39346856), (-0.33012997, 225.29125, 0.14026623)-0.43881481, 0.88756236, 93.53095
35generate(-0.76517904, 0.30949045, -0.56454999), (463.35451, 0.30949045, -0.59209629), (-0.74406831, 518.73304, -0.56454999)-0.7440683, 0.35727534, 477.1026
36generate(-0.01922097, -0.98272699, 0.18406034), (207.04106, 0.20328414, -0.18409024), (-0.96165812, 572.55127, 0.9789311)0.01893254, 0.20331121, 212.54584
37generate(-0.80788407, -0.39328253, -0.43892161), (514.88169, 0.32143146, 0.33020015), (-0.8874963, 447.88369, 0.49396876)-0.85807734, -0.14035007, 563.41293
38generate(-0.59177988, 0.74430199, -0.30953372), (261.18544, 0.74430199, 0.35707532), (-0.56436846, 238.12149, -0.30953372)-0.56436846, -0.76529545, 917.04212
39generate(0.33044296, 0.85792342, 0.39341436), (-203.44809, 0.88750304, -0.14060529), (-0.4388263, 233.14891, -0.32116322)0.4941635, -0.80787166, 784.72989
40generate(0.68430382, -0.20943919, 0.69847226), (-236.91116, 0.55313561, -0.475064), (-0.68436481, 439.83788, 0.47515184)0.85466334, -0.20923983, 349.32724
41generate(0.20313838, -0.18425095, -0.96165815), (572.59558, -0.97896101, -0.01892042), (-0.20316829, 379.89275, 0.01923898)0.98269711, -0.18421795, 385.53126
42generate(0.32122961, 0.33026198, -0.88754637), (447.92634, -0.4940277, 0.85802332), (0.14047284, 29.04845, 0.80792832)0.39334845, 0.43878106, 77.66534
43generate(0.74425197, 0.3572772, -0.56430666), (238.07184, 0.30941638, 0.56432755), (0.76537306, -324.55397, 0.59190414)-0.74423613, 0.30945446, 331.32258
44generate(0.88760293, -0.14053941, -0.43864531), (233.04386, 0.32103881, -0.49413015), (0.8079415, -192.24797, -0.33029549)-0.85795341, -0.39347278, 795.95728
45generate(0.55317634, -0.47522221, -0.68422204), (439.7909, -0.47522221, -0.85459723), (0.20935002, 243.12405, -0.68422203)0.20935002, -0.69857911, 829.46009
46generate(0.00016074, 1.496E-5, -0.99999999), (592.4746, 0.99999998, -0.00014574), (0.00016073, -0.05089, -0.00014575)-0.99999999, -1.499E-5, 592.52782
47generate(0.35747906, 0.56426572, -0.74418608), (344.63665, 0.56426572, -0.76545067), (-0.30933714, 312.24349, -0.74418607)-0.30933714, -0.59202839, 865.409
48generate(0.88760293, 0.32103881, -0.3302955), (117.76975, -0.1405394, -0.49413016), (-0.85795341, 620.65059, -0.4386453)0.8079415, -0.39347277, 570.73623
49generate(0.85791918, -0.39353444, -0.33031096), (225.39626, -0.14039867, 0.43886006), (-0.88751905, 498.96229, 0.4942296)0.80779483, 0.32125475, 115.73726
50generate(0.30944974, -0.59193809, -0.7442111), (518.77999, 0.56449343, 0.74415922), (-0.35717534, 115.34767, 0.76523724)-0.30957446, 0.56442503, 129.20521
51generate(-0.01922097, 0.20328414, 0.97893111), (-320.4788, -0.98272699, -0.18409023), (0.01893254, 304.8419, 0.18406034)-0.96165812, 0.20331121, 469.27758
52generate(-0.209431, -0.47487533, 0.85477019), (-139.30088, -0.69843149, 0.68444232), (0.20912238, 52.95692, -0.68434795)-0.55320171, -0.47501132, 839.60728
53generate(-0.77704396, -0.46909162, 0.41970912), (136.80349, 0.04034742, 0.62830022), (0.77692401, -300.07072, -0.62815187)0.62063828, -0.46929025, 659.18158
54generate(-0.93763804, 0.21264239, 0.27498751), (126.26745, 0.21264239, -0.27493005), (0.93765488, -266.36881, 0.2749875)0.93765488, 0.21256809, 177.34266
55generate(-0.46927767, 0.62819346, 0.62060571), (-156.34854, -0.41965237, -0.77701497), (0.46919039, 107.48775, 0.77696226)-0.04025807, 0.62825865, 59.97553
56generate(-0.18407814, -0.01904816, 0.98272703), (-266.19139, 0.96168803, 0.2031564), (0.18407502, -106.28369, -0.20315358)0.978961, -0.01907826, 344.26339
57generate(-0.46927768, -0.41965237, 0.77696226), (-74.86212, 0.62819346, -0.77701497), (-0.04025808, 184.15122, 0.6206057)0.4691904, 0.62825866, 8.91843
58generate(-0.85481095, -0.20922439, 0.47489304), (85.75491, -0.20922439, -0.69849761), (-0.68434366, 582.37417, 0.47489304)-0.68434365, 0.55330856, 230.35968
59generate(-0.80788407, 0.32143146, 0.49396877), (-6.30758, -0.39328252, 0.33020015), (-0.85807734, 538.05457, -0.43892161)-0.8874963, -0.14035006, 702.56285
60generate(-0.3933484, 0.43896684, 0.80782743), (-223.82236, 0.33038115, 0.88745297), (-0.32136508, 112.44061, -0.85797747)0.14048251, -0.49410457, 772.95922

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Components

#1: Protein VP1


Mass: 32832.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VIRION OF HUMAN ENTEROVIRUS 71 / Source: (natural) HUMAN ENTEROVIRUS 71 / Variant: ISOLATE MY104-9-SAR-97 / References: UniProt: A9X4C2
#2: Protein VP2


Mass: 27800.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VIRION OF HUMAN ENTEROVIRUS 71 / Source: (natural) HUMAN ENTEROVIRUS 71 / Variant: ISOLATE MY104-9-SAR-97 / References: UniProt: A9X4C2
#3: Protein VP3


Mass: 26524.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VIRION OF HUMAN ENTEROVIRUS 71 / Source: (natural) HUMAN ENTEROVIRUS 71 / Variant: ISOLATE MY104-9-SAR-97 / References: UniProt: A9X4C2
#4: Protein VP4


Mass: 7501.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VIRION OF HUMAN ENTEROVIRUS 71 / Source: (natural) HUMAN ENTEROVIRUS 71 / Variant: ISOLATE MY104-9-SAR-97 / References: UniProt: A9X4C2, UniProt: B2ZUN0*PLUS
#5: Chemical ChemComp-W71 / 5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE / COMPOUND IV


Mass: 342.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N2O3
Nonpolymer details5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE (W71): WIN 51711

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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: 4.55 Å3/Da / Density % sol: 73.3 % / Description: NONE
Crystal growpH: 8.5
Details: THE CRYSTALLIZATION DROPS WERE PREPARED BY MIXING 0.83UL OF EV71 AT 2MG/ML IN PBS WITH 0.17UL OF 0.2M SODIUM CITRATE, 0.1M TRIS PH8.5, 30% V/V PEG 400. THE WELL SOLUTION CONTAINED 1.8M ...Details: THE CRYSTALLIZATION DROPS WERE PREPARED BY MIXING 0.83UL OF EV71 AT 2MG/ML IN PBS WITH 0.17UL OF 0.2M SODIUM CITRATE, 0.1M TRIS PH8.5, 30% V/V PEG 400. THE WELL SOLUTION CONTAINED 1.8M SODIUM ACETATE AND 0.1M BIS-TRIS PROPANE PH7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9787
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3.2→33.2 Å / Num. obs: 353681 / % possible obs: 66.8 % / Observed criterion σ(I): 0.8 / Redundancy: 2.5 % / Rmerge(I) obs: 0.33 / Net I/σ(I): 2.5
Reflection shellResolution: 3.2→3.35 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 0.81 / % possible all: 44

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
GLRFphasing
PHASERphasing
CNS1.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AED

4aed


Resolution: 3.2→33.2 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0
Isotropic thermal model: CONSTRAINED 2 B FACTORS PER RESIDUE
σ(F): 0.8
RfactorNum. reflection% reflection
Rwork0.2491 --
obs0.2491 353681 66.8 %
Solvent computationSolvent model: BULK SOLVENT
Displacement parametersBiso mean: 36.9 Å2
Refinement stepCycle: LAST / Resolution: 3.2→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6507 0 25 0 6532
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008474
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.49016
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINS
LS refinement shellResolution: 3.2→3.35 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.3547 15538 -
obs--44 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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