4WT9

APO CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH E86Q E87Q S15G C223H V321I AND DELTA8 MUTATIONS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4E76PDB entry 4E76

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.9289NS5B AT 4.08 MG/ML IN 20 MM TRIS PH 8, 200 MM NACL, 20% GLYCEROL, 2 MM TCEP, 200 MM IMIDAZOLE AGAINST 30% PEG 550 MME, 0.1 M HEPES PH 7.5, 50 MM MAGNESIUM CHLORIDE WITH 15% ETHYLENE GLYCOL AS CRYO-PROTECTANT, CRYSTAL TRACKING ID 232769E7
Crystal Properties
Matthews coefficientSolvent content
470

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.37α = 90
b = 140.37β = 90
c = 92.23γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.07809APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.55098.50.0840.09916.623.635345-346.96
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5698.60.7060.0212.63.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 4E762.55035345177498.50.1950.1930.245RANDOM33.09
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.740.871.74-2.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.601
r_dihedral_angle_4_deg18.829
r_dihedral_angle_3_deg16.116
r_dihedral_angle_1_deg6.287
r_angle_refined_deg1.529
r_angle_other_deg0.917
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.601
r_dihedral_angle_4_deg18.829
r_dihedral_angle_3_deg16.116
r_dihedral_angle_1_deg6.287
r_angle_refined_deg1.529
r_angle_other_deg0.917
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4165
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms31

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing