3HKY

HCV NS5B polymerase genotype 1b in complex with 1,5 benzodiazepine 6


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.752935-8% PEG 6000, 100mM Mg-Salts, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9157.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.274α = 90
b = 107.679β = 90
c = 133.573γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2008-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0073SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.944.999.90.0866.5120846120846
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.951000.186.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1NB41.944.91198781198789671000.184230.184230.184030.20861RANDOM42.899
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]
2.78-0.94-1.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.946
r_dihedral_angle_4_deg14.812
r_dihedral_angle_3_deg12.76
r_scangle_it6.328
r_dihedral_angle_1_deg5.574
r_scbond_it4.83
r_mcangle_it3.075
r_mcbond_it2.657
r_angle_refined_deg1.319
r_angle_other_deg0.781
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.946
r_dihedral_angle_4_deg14.812
r_dihedral_angle_3_deg12.76
r_scangle_it6.328
r_dihedral_angle_1_deg5.574
r_scbond_it4.83
r_mcangle_it3.075
r_mcbond_it2.657
r_angle_refined_deg1.319
r_angle_other_deg0.781
r_mcbond_other0.673
r_symmetry_vdw_other0.242
r_symmetry_vdw_refined0.214
r_nbd_refined0.202
r_nbd_other0.179
r_nbtor_refined0.179
r_xyhbond_nbd_refined0.147
r_symmetry_hbond_refined0.146
r_nbtor_other0.084
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8752
Nucleic Acid Atoms
Solvent Atoms672
Heterogen Atoms124

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling