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

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Basic information

Entry
Database: PDB / ID: 3zfe
TitleHuman enterovirus 71 in complex with capsid binding inhibitor WIN51711
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / EV71 / 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 / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...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 / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / 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 ...Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / 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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Viral coat protein subunit / Few Secondary Structures / Irregular / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / 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
SPHINGOSINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHUMAN ENTEROVIRUS 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.2Dec 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_conn_angle / pdbx_struct_oper_list / struct_conn / 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_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _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 / _struct_conn.ptnr2_label_seq_id / _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)95,13112
Polymers94,6594
Non-polymers4738
Water0
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,707,884720
Polymers5,679,511240
Non-polymers28,373480
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
  • 476 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)475,65760
Polymers473,29320
Non-polymers2,36440
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
  • 571 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)570,78872
Polymers567,95124
Non-polymers2,83748
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)594.500, 594.500, 594.500
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(0.742488, 0.309416, 0.59409), (0.358155, 0.566058, -0.742472), (-0.566037, 0.764065, 0.309454)-274.5155, 344.6636, 281.5975
3generate(0.858823, -0.39532, -0.325731), (-0.135845, 0.437319, -0.88897), (0.493895, 0.807735, 0.321859)224.22945, 500.85931, 115.89023
4generate(0.566162, 0.742345, -0.358254), (-0.764006, 0.309457, -0.566115), (-0.30937, 0.594248, 0.742381)116.23511, 465.46707, 74.43829
5generate(0.437245, -0.807837, 0.395193), (0.889004, 0.321844, -0.325654), (0.135862, 0.493737, 0.85891)21.27342, 115.75485, -27.94919
6generate(0.309449, 0.566224, 0.763928), (-0.594124, 0.742395, -0.309574), (-0.742447, -0.358052, 0.566155)-325.26959, 262.70847, 354.65222
7generate(0.321833, -0.493693, 0.807869), (0.325682, 0.858927, 0.395134), (-0.888998, 0.135919, 0.437241)-193.01926, -204.35995, 362.17584
8generate(0.309449, -0.594124, -0.742447), (0.566224, 0.742395, -0.358052), (0.763928, -0.309574, 0.566155)520.06201, 116.12817, 129.04291
9generate(0.321833, 0.325682, -0.888998), (-0.493693, 0.858927, 0.135919), (0.807869, 0.395134, 0.437241)450.66113, 31.0227, 78.34842
10generate(0.437245, 0.889004, 0.135862), (-0.807837, 0.321844, 0.493737), (0.395193, -0.325654, 0.85891)-108.39534, -6.26776, 53.31561
11generate(0.566162, -0.764006, -0.30937), (0.742345, 0.309457, 0.594248), (-0.358254, -0.566115, 0.742381)312.83804, -274.57153, 249.90004
12generate(0.858822, -0.135845, 0.493895), (-0.39532, 0.437319, 0.807735), (-0.325731, -0.88897, 0.321859)-181.76044, -223.9902, 481.00995
13generate(0.742488, 0.358155, -0.566037), (0.309416, 0.566058, 0.764065), (0.59409, -0.742472, 0.309454)239.77391, -325.30191, 331.86142
14generate(0.889054, 0.321642, -0.325715), (-0.135985, -0.493796, -0.858857), (-0.437104, 0.807882, -0.395258)115.80437, 622.45154, 573.22925
15generate(0.680451, -0.206898, 0.702952), (0.558943, -0.473752, -0.680511), (0.473839, 0.855992, -0.206699)-239.51898, 438.56064, 349.33191
16generate(0.000161, 1, -0.000146), (1.5E-5, -0.000146, -1), (-1, 0.000161, -1.5E-5)0.04202, 594.51886, 594.48358
17generate(-0.188405, -0.020026, 0.981887), (0.959713, 0.208461, 0.188402), (-0.208458, 0.977826, -0.020056)-265.9169, -109.06966, 346.77805
18generate(-0.020199, -0.981887, 0.188386), (0.208588, -0.188417, -0.959682), (0.977795, 0.019911, 0.208616)205.84184, 573.45441, 210.881
19generate(0.208443, -0.188578, -0.959682), (-0.977826, -0.019899, -0.208473), (0.020217, 0.981857, -0.188544)573.4989, 383.55765, 388.73077
20generate(-0.395135, 0.437426, 0.807768), (0.325802, 0.888905, -0.321968), (-0.858881, 0.135929, -0.49377)-224.04736, 113.5387, 776.20056
21generate(-0.206891, -0.702911, -0.680495), (-0.473563, 0.680589, -0.559009), (0.856098, 0.206582, -0.473698)582.9267, 366.27927, 508.08517
22generate(-0.493759, 0.858922, 0.135712), (-0.807792, -0.395254, -0.437274), (-0.321925, -0.32555, 0.889013)31.12584, 516.17285, 143.82626
23generate(-0.473721, -0.856032, 0.206801), (0.680446, -0.206691, 0.703017), (-0.55905, 0.473769, 0.680412)245.11075, -239.57776, 155.99689
24generate(-0.493759, -0.807792, -0.321925), (0.858922, -0.395254, -0.32555), (0.135712, -0.437274, 0.889013)478.62802, 224.12402, 93.63434
25generate(-0.473721, 0.680446, -0.55905), (-0.856032, -0.206691, 0.473769), (0.206801, 0.703017, 0.680412)366.34119, 86.38939, 11.608
26generate(-0.206891, -0.473563, 0.856098), (-0.702911, 0.680589, 0.206582), (-0.680495, -0.559009, -0.473698)-140.89661, 55.50121, 842.13208
27generate(-0.395135, 0.325802, -0.858881), (0.437426, 0.888905, 0.135929), (0.807768, -0.321968, -0.49377)541.14124, -108.43706, 600.81073
28generate(-0.020199, 0.208588, 0.977795), (-0.981887, -0.188417, 0.019911), (0.188386, -0.959682, 0.208616)-321.65634, 305.96323, 467.56311
29generate(0.208443, -0.977826, 0.020217), (-0.188578, -0.019899, 0.981857), (-0.959682, -0.208473, -0.188544)247.6519, -265.89642, 703.63104
30generate(0.000161, 1.5E-5, -1), (1, -0.000146, 0.000161), (-0.000146, -1, -1.5E-5)594.47437, -0.05119, 594.52802
31generate(-0.188405, 0.959713, -0.208458), (-0.020026, 0.208461, 0.977826), (0.981887, 0.188402, -0.020056)126.86426, -321.67682, 288.60437
32generate(0.680451, 0.558943, 0.473839), (-0.206898, -0.473752, 0.855992), (0.702952, -0.680511, -0.206699)-247.67944, -140.8204, 539.0343
33generate(0.889054, -0.135985, -0.437104), (0.321642, -0.493796, 0.807882), (-0.325715, -0.858857, -0.395258)232.26436, -192.98245, 798.9104
34generate(0.325863, 0.858828, 0.3952), (0.888955, -0.136051, -0.437286), (-0.321767, 0.493829, -0.807812)-204.40164, 232.36978, 787.46436
35generate(0.630442, -0.77551, -0.03313), (-0.615147, -0.473106, -0.630656), (0.473391, 0.417984, -0.775336)181.03806, 586.42212, 668.49756
36generate(-0.135778, 0.437138, -0.889069), (-0.493862, -0.807805, -0.321734), (-0.858852, 0.395378, 0.325583)500.92056, 478.55927, 370.33295
37generate(-0.473299, -0.418116, 0.775321), (0.630608, -0.775374, -0.033163), (0.615048, 0.473212, 0.630672)-73.98497, 181.00912, 8.06931
38generate(-0.807825, 0.322035, 0.493634), (-0.395068, 0.325621, -0.85898), (-0.437381, -0.888947, -0.135796)-6.25093, 541.20251, 702.87708
39generate(-0.775403, -0.473113, 0.418172), (0.033253, 0.630715, 0.775282), (-0.630566, 0.61508, -0.473312)138.33307, -299.65359, 664.35315
40generate(-0.807825, -0.395068, -0.437381), (0.322035, 0.325621, -0.888947), (0.493634, -0.85898, -0.135796)516.19897, 450.61801, 563.4386
41generate(-0.775403, 0.033253, -0.630566), (-0.473113, 0.630715, 0.61508), (0.418172, 0.775282, -0.473312)536.16248, -154.18509, 488.93588
42generate(-0.473299, 0.630607, 0.615048), (-0.418116, -0.775374, 0.473212), (0.775321, -0.033163, 0.630673)-154.12793, 105.61368, 58.28876
43generate(-0.135778, -0.493862, -0.858852), (0.437138, -0.807805, 0.395378), (-0.88907, -0.321734, 0.325583)622.42883, 21.20088, 478.77054
44generate(0.630442, -0.615147, 0.473391), (-0.77551, -0.473106, 0.417984), (-0.03313, -0.630656, -0.775336)-69.86113, 138.43236, 894.15125
45generate(0.325863, 0.888955, -0.321767), (0.858827, -0.136051, 0.493829), (0.3952, -0.437286, -0.807812)113.43176, -181.70166, 818.53723
46generate(0.959713, 0.208316, 0.188562), (0.208316, -0.977856, 0.020044), (0.188562, 0.020044, -0.981857)-109.12086, 247.75259, 860.37756
47generate(0.358357, 0.565997, -0.742421), (0.565997, -0.764142, -0.309337), (-0.742421, -0.309337, -0.594215)344.62048, 312.867, 869.05017
48generate(0.03322, 0.630549, 0.775419), (0.630549, -0.615179, 0.473205), (0.775419, 0.473205, -0.41804)-299.68591, -69.78859, 456.09204
49generate(0.20908, -0.269247, 0.940082), (-0.269247, -0.940027, -0.209329), (0.940082, -0.209328, -0.269054)-268.64255, 414.63776, 464.28043
50generate(0.558984, -0.47391, -0.680368), (-0.47391, -0.855926, 0.206809), (-0.680368, 0.206809, -0.703058)438.51331, 245.11948, 834.06775
51generate(-0.593966, 0.742538, -0.309534), (0.742538, 0.357953, -0.566099), (-0.309534, -0.566099, -0.763987)262.64655, 239.82343, 919.78992
52generate(-0.702845, 0.680594, 0.206788), (0.680594, 0.558903, 0.473681), (0.206788, 0.473681, -0.856058)55.39807, -247.62341, 735.3761
53generate(-0.418305, -0.775267, 0.47322), (-0.775267, 0.033286, -0.630732), (0.47322, -0.630732, -0.614981)105.62242, 536.2124, 748.62756
54generate(-0.26935, -0.940039, -0.209138), (-0.940039, 0.209461, 0.269099), (-0.209138, 0.269099, -0.940111)414.569, 130.17398, 863.18567
55generate(-0.76387, 0.30949, -0.56628), (0.30949, -0.594282, -0.742304), (-0.56628, -0.742304, 0.358152)465.51697, 520.01465, 478.32224
56generate(-0.940052, 0.209271, 0.269202), (0.209271, -0.269144, 0.940069), (0.269202, 0.940069, 0.209196)130.15715, -268.67935, 179.92221
57generate(-0.856139, -0.206684, 0.47358), (-0.206684, -0.702977, -0.68049), (0.47358, -0.68049, 0.559115)86.48868, 582.90393, 228.15616
58generate(-0.615114, -0.473291, -0.630548), (-0.473291, -0.417927, 0.775427), (-0.630548, 0.775427, 0.033041)586.396, -74.0612, 413.52957
59generate(-0.977795, -0.020072, -0.2086), (-0.020072, -0.981857, 0.18856), (-0.2086, 0.18856, 0.959652)383.63538, 205.74115, 21.04047
60generate(-0.981918, -0.188244, 0.020038), (-0.188244, 0.959713, -0.208604), (0.020038, -0.208604, -0.977795)305.8855, 126.90628, 916.18195

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Components

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Protein , 4 types, 4 molecules ABCD

#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

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Non-polymers , 3 types, 8 molecules

#5: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 4.5 Å3/Da / Density % sol: 73 % / 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: Aug 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.7→30.4 Å / Num. obs: 692970 / % possible obs: 74.9 % / Observed criterion σ(I): 0.5 / Redundancy: 1.9 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 3.05
Reflection shellResolution: 2.7→2.82 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 0.56 / % possible all: 35.9

-
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: 2.7→30.4 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: NA / σ(F): 0.5
RfactorNum. reflection% reflection
Rwork0.2402 --
obs0.2402 692970 74.9 %
Solvent computationSolvent model: BULK SOLVENT
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6501 0 28 0 6529
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005233
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_deg1.28602
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: 2.7→2.82 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.4099 34593 -
obs--35.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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