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- PDB-2x5i: Crystal structure echovirus 7 -

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Basic information

Entry
Database: PDB / ID: 2x5i
TitleCrystal structure echovirus 7
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / CAPSID PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / 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 / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Picornavirus coat protein VP4 superfamily / 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 ...Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Picornavirus coat protein VP4 superfamily / 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 / 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
LAURIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesHUMAN ECHOVIRUS 7
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPlevka, P. / Hafenstein, S. / Zhang, Y. / Bowman, V.D. / Chipman, P.R. / Bator, C.M. / Rossmann, M.G.
CitationJournal: J Virol / Year: 2010
Title: Interaction of decay-accelerating factor with echovirus 7.
Authors: Pavel Plevka / Susan Hafenstein / Katherine G Harris / Javier O Cifuente / Ying Zhang / Valorie D Bowman / Paul R Chipman / Carol M Bator / Feng Lin / M Edward Medof / Michael G Rossmann /
Abstract: Echovirus 7 (EV7) belongs to the Enterovirus genus within the family Picornaviridae. Many picornaviruses use IgG-like receptors that bind in the viral canyon and are required to initiate viral ...Echovirus 7 (EV7) belongs to the Enterovirus genus within the family Picornaviridae. Many picornaviruses use IgG-like receptors that bind in the viral canyon and are required to initiate viral uncoating during infection. However, in addition, some of the enteroviruses use an alternative or additional receptor that binds outside the canyon. Decay-accelerating factor (DAF) has been identified as a cellular receptor for EV7. The crystal structure of EV7 has been determined to 3.1-Å resolution and used to interpret the 7.2-Å-resolution cryo-electron microscopy reconstruction of EV7 complexed with DAF. Each DAF binding site on EV7 is near a 2-fold icosahedral symmetry axis, which differs from the binding site of DAF on the surface of coxsackievirus B3, indicating that there are independent evolutionary processes by which DAF was selected as a picornavirus accessory receptor. This suggests that there is an advantage for these viruses to recognize DAF during the initial process of infection.
History
DepositionFeb 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,4135
Polymers96,2124
Non-polymers2001
Water00
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,784,759300
Polymers5,772,740240
Non-polymers12,01960
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
  • 482 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)482,06325
Polymers481,06220
Non-polymers1,0025
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
  • 578 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)578,47630
Polymers577,27424
Non-polymers1,2026
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)297.100, 297.700, 300.600
Angle α, β, γ (deg.)119.00, 100.10, 108.40
Int Tables number1
Space group name H-MP1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.804384, -0.385393, -0.452149), (-0.57654, -0.322653, -0.750664), (0.143413, 0.864504, -0.481731)
3generate(0.804384, -0.57654, 0.143413), (-0.385393, -0.322653, 0.864504), (-0.452149, -0.750664, -0.481731)
4generate(0.385527, -0.520453, -0.761904), (-0.520453, -0.804499, 0.286198), (-0.761904, 0.286198, -0.581028)
5generate(0.500907, -0.639323, 0.583403), (0.086227, 0.707572, 0.70136), (-0.861195, -0.301012, 0.409555)
6generate(0.855185, 0.517587, -0.027611), (-0.238, 0.344798, -0.908004), (-0.460451, 0.783082, 0.418052)
7generate(0.312222, -0.949976, -0.007981), (0.946123, 0.310175, 0.092964), (-0.085838, -0.036577, 0.995637)
8generate(0.797701, 0.179285, 0.575787), (0.595551, -0.38434, -0.705409), (0.094828, 0.905616, -0.413361)
9generate(0.620869, 0.132495, -0.772637), (0.599474, -0.715342, 0.35905), (-0.505127, -0.686098, -0.523561)
10generate(0.620869, 0.599474, -0.505127), (0.132495, -0.715342, -0.686098), (-0.772637, 0.35905, -0.523561)
11generate(0.081354, -0.869385, -0.487393), (0.420605, -0.41339, 0.807589), (-0.903589, -0.270701, 0.332036)
12generate(0.496777, -0.172197, 0.850624), (0.692483, 0.669448, -0.2689), (-0.523145, 0.722626, 0.45181)
13generate(-0.800627, -0.59097, -0.098752), (0.580884, -0.805986, 0.113843), (-0.14687, 0.033782, 0.988579)
14generate(-0.317456, 0.413862, 0.853194), (0.948264, 0.134603, 0.287537), (0.004158, 0.900333, -0.435181)
15generate(-0.371605, 0.726401, -0.578144), (0.726401, -0.160307, -0.668314), (-0.578144, -0.668314, -0.468088)
16generate(0.074148, 0.863861, 0.498244), (0.556687, 0.378674, -0.739395), (-0.827406, 0.332191, -0.452822)
17generate(-0.366952, 0.12343, -0.922015), (0.12343, -0.975934, -0.179773), (-0.922015, -0.179773, 0.342886)
18generate(-0.498562, -0.69549, 0.517425), (0.636169, 0.111904, 0.763392), (-0.588834, 0.709768, 0.386658)
19generate(-0.800627, 0.580884, -0.14687), (-0.59097, -0.805986, 0.033782), (-0.098752, 0.113843, 0.988579)
20generate(-0.999978, -0.005838, -0.003294), (-0.005838, 0.517014, 0.855957), (-0.003294, 0.855957, -0.517037)
21generate(-0.801473, 0.38442, 0.458108), (-0.18002, 0.575412, -0.797805), (-0.570293, -0.721888, -0.391974)
22generate(-0.499085, -0.092666, 0.861584), (0.165904, 0.965656, 0.199962), (-0.850523, 0.242738, -0.466571)
23generate(-0.224468, 0.967086, -0.11983), (-0.394611, -0.202642, -0.896224), (-0.891008, -0.153887, 0.42711)
24generate(-0.755307, -0.329118, -0.566738), (-0.329118, -0.557326, 0.762278), (-0.566738, 0.762278, 0.312634)
25generate(0.312222, 0.946123, -0.085838), (-0.949976, 0.310175, -0.036577), (-0.007981, 0.092964, 0.995637)
26generate(-0.306642, -0.499805, -0.81004), (-0.948219, 0.234414, 0.214313), (0.08277, 0.833813, -0.545806)
27generate(-0.074671, -0.420842, 0.904055), (-0.867146, 0.475077, 0.149528), (-0.492424, -0.772783, -0.400406)
28generate(-0.306642, -0.948219, 0.08277), (-0.499805, 0.234414, 0.833813), (-0.81004, 0.214313, -0.545806)
29generate(0.311899, 0.495678, 0.810569), (-0.417605, 0.837822, -0.351654), (-0.85342, -0.228817, 0.468313)
30generate(0.081354, 0.420605, -0.903589), (-0.869385, -0.41339, -0.270701), (-0.487393, 0.807589, 0.332036)
31generate(-0.762837, 0.646509, -0.010344), (0.646509, 0.762385, -0.028198), (-0.010344, -0.028198, -0.999549)
32generate(-0.987835, 0.076451, -0.135412), (0.076451, -0.519522, -0.85103), (-0.135412, -0.85103, 0.507358)
33generate(-0.858096, 0.238973, 0.454491), (0.238973, -0.597557, 0.765387), (0.454491, 0.765387, 0.455654)
34generate(-0.622691, -0.126055, 0.772248), (-0.126055, -0.957886, -0.258), (0.772248, -0.258, 0.580577)
35generate(-0.317456, 0.948264, 0.004158), (0.413862, 0.134603, 0.900333), (0.853194, 0.287537, -0.435181)
36generate(-0.801473, -0.18002, -0.570293), (0.38442, 0.575412, -0.721888), (0.458108, -0.797805, -0.391974)
37generate(0.37439, 0.925585, 0.055892), (0.925585, -0.376663, 0.03764), (0.055892, 0.03764, -0.997727)
38generate(-0.224468, -0.394611, -0.891008), (0.967086, -0.202642, -0.153887), (-0.11983, -0.896224, 0.42711)
39generate(-0.080831, -0.55645, 0.82694), (0.87267, -0.440361, -0.211018), (0.481573, 0.704589, 0.521192)
40generate(-0.37997, -0.923489, -0.052823), (0.524196, -0.167926, -0.834877), (0.76213, -0.344918, 0.547896)
41generate(0.219211, 0.398738, 0.89048), (0.398738, -0.869594, 0.291228), (0.89048, 0.291228, -0.349617)
42generate(0.074148, 0.556687, -0.827406), (0.863861, 0.378674, 0.332191), (0.498244, -0.739395, -0.452822)
43generate(0.987813, -0.070613, 0.138706), (-0.070613, -0.997492, -0.004927), (0.138706, -0.004927, -0.990321)
44generate(0.855185, -0.238, -0.460451), (0.517587, 0.344798, 0.783082), (-0.027611, -0.908004, 0.418052)
45generate(0.759079, -0.650852, 0.013801), (0.329854, 0.366254, -0.870089), (0.561245, 0.665019, 0.492701)
46generate(0.311899, -0.417605, -0.85342), (0.495678, 0.837822, -0.228817), (0.810569, -0.351654, 0.468313)
47generate(0.369261, -0.723247, 0.583575), (-0.117138, -0.65917, -0.742815), (0.921914, 0.205934, -0.328125)
48generate(0.797701, 0.595551, 0.094828), (0.179285, -0.38434, 0.905616), (0.575787, -0.705409, -0.413361)
49generate(0.229702, -0.965374, 0.123653), (-0.965374, -0.242136, -0.097073), (0.123653, -0.097073, -0.987566)
50generate(0.759079, 0.329854, 0.561245), (-0.650852, 0.366254, 0.665019), (0.013801, -0.870089, 0.492701)
51generate(0.500907, 0.086227, -0.861195), (-0.639323, 0.707572, -0.301012), (0.583403, 0.70136, 0.409555)
52generate(0.496777, 0.692483, -0.523145), (-0.172197, 0.669448, 0.722626), (0.850624, -0.2689, 0.45181)
53generate(-0.074671, -0.867146, -0.492424), (-0.420842, 0.475077, -0.772783), (0.904055, 0.149528, -0.400406)
54generate(0.369261, -0.117138, 0.921914), (-0.723247, -0.65917, 0.205934), (0.583575, -0.742815, -0.328125)
55generate(-0.852259, -0.522169, 0.031535), (-0.522169, 0.845528, -0.111455), (0.031535, -0.111455, -0.993269)
56generate(-0.37997, 0.524196, 0.76213), (-0.923489, -0.167926, -0.344918), (-0.052823, -0.834877, 0.547896)
57generate(-0.498562, 0.636169, -0.588834), (-0.69549, 0.111904, 0.709768), (0.517425, 0.763392, 0.386658)
58generate(-0.080831, 0.87267, 0.481573), (-0.55645, -0.440361, 0.704589), (0.82694, -0.211018, 0.521192)
59generate(-0.499085, 0.165904, -0.850523), (-0.092666, 0.965656, 0.242738), (0.861584, 0.199962, -0.466571)
60generate(-0.619083, -0.596467, 0.510846), (-0.596467, -0.06601, -0.799919), (0.510846, -0.799919, -0.314907)
DetailsTHE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR ICOSAHEDRAL POINT SYMMETRY (SCHOENFLIES SYMBOL = I). THIS IS A MATRIX TO BRING THE MODEL TO STANDARD ORIENTATION (MATRIX IS IN O/USF FORMAT) - AS PROVIDED BY THE DEPOSITOR: ROT_MAT R 12 (3F15.9) 0.8323242 0.3443569 0.4343440 -0.3126505 0.9387187 -0.1451101 -0.4576965 -0.0150192 0.8889817 0.0000000 0.0000000 0.0000000

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Components

#1: Protein VP1


Mass: 33313.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE ECHOVIRUS7 (WALLACE) WAS PURCHASED FROM THE AMERICAN TYPE CULTURE COLLECTION.
Source: (natural) HUMAN ECHOVIRUS 7 / Strain: WALLACE / References: UniProt: Q6W9E5
#2: Protein VP2


Mass: 29072.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE ECHOVIRUS7 (WALLACE) WAS PURCHASED FROM THE AMERICAN TYPE CULTURE COLLECTION.
Source: (natural) HUMAN ECHOVIRUS 7 / Strain: WALLACE / References: UniProt: Q6W9E5
#3: Protein VP3


Mass: 26226.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE ECHOVIRUS7 (WALLACE) WAS PURCHASED FROM THE AMERICAN TYPE CULTURE COLLECTION.
Source: (natural) HUMAN ECHOVIRUS 7 / Strain: WALLACE / References: UniProt: Q6W9E5
#4: Protein VP4


Mass: 7599.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE ECHOVIRUS7 (WALLACE) WAS PURCHASED FROM THE AMERICAN TYPE CULTURE COLLECTION.
Source: (natural) HUMAN ECHOVIRUS 7 / Strain: WALLACE / References: UniProt: Q6W9E5
#5: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2

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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: 3.64 Å3/Da / Density % sol: 66.2 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP, BOTTOM SOLUTION CONTAINED 0.25% PEG 8000, 0.25% GLYCEROL, 400 MM NACL, 150 MM CACL, 100 MM TRIS PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→25 Å / Num. obs: 655131 / % possible obs: 45.9 % / Observed criterion σ(I): 2 / Redundancy: 1.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.95
Reflection shellResolution: 3.1→3.24 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 1.98 / % possible all: 32.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
GLRFphasing
CNSphasing
CNS1.21refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1COV

1cov


Resolution: 3.1→25 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: NONE / σ(F): 0 / Stereochemistry target values: CRYSTALLOGRAPHIC RESIDUAL
RfactorNum. reflection% reflection
Rwork0.2882 --
obs0.2882 655131 46.1 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 7.03341 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1--13.32 Å20.22 Å2-0.27 Å2
2--5.54 Å2-12.84 Å2
3---7.78 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.7 Å
Refinement stepCycle: LAST / Resolution: 3.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6526 0 14 0 6540
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it1.72
X-RAY DIFFRACTIONc_scangle_it2.692.5
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 3.1→3.24 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.3655 57383 -
obs--32.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DAO_XPLOR_PAR.TXTDAO_XPLOR_PAR.TXT

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