3D5M

Crystal structure of HCV NS5B polymerase with a novel pyridazinone inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429820% PEG 4K, 50 MM AMMONIUM SULFATE, 100 MM SODIUM ACETATE, 5 MM DTT, PH 4.7, TRANSFERRED TO PH 7.4 FOR SOAKING AND DATA COLLECTION, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2645.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.304α = 90
b = 106.765β = 90
c = 126.254γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMIRRORS2006-08-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
12.22999.70.0118.16.4597865978641.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.2899.5

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 REPLACEMENTTHROUGHOUTHCV POLYMERASE2.2295961059610298199.710.21070.21070.208030.26137RANDOM48.503
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]
0.082.28-2.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.289
r_dihedral_angle_3_deg15.25
r_dihedral_angle_4_deg12.854
r_dihedral_angle_1_deg5.6
r_scangle_it2.76
r_mcangle_it2.189
r_scbond_it2.062
r_mcbond_it1.447
r_angle_refined_deg1.156
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.289
r_dihedral_angle_3_deg15.25
r_dihedral_angle_4_deg12.854
r_dihedral_angle_1_deg5.6
r_scangle_it2.76
r_mcangle_it2.189
r_scbond_it2.062
r_mcbond_it1.447
r_angle_refined_deg1.156
r_nbtor_refined0.296
r_nbd_refined0.195
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.139
r_symmetry_hbond_refined0.1
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8679
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing