3CWJ

Crystal structure of hcv ns5b polymerase with a novel pyridazinone inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.629820% PEG 4000, 50 MM AMMONIUM SULFATE, 100 MM SODIUM ACETATE, 5 MM DTT, PH 4.7, TRANSFERRED TO PH 7.6 FOR SOAKING, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2645.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.107α = 90
b = 106.393β = 90
c = 126.731γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMIRRORS2006-07-27MSINGLE 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
12.429.1292.480.128.53.3427024270238.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.42944.41038

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 POLYMERASE2.429.124270240579212192.480.240330.240330.237280.29974RANDOM45.224
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]
-1.233.72-2.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.083
r_dihedral_angle_4_deg15.638
r_dihedral_angle_3_deg15.492
r_dihedral_angle_1_deg5.566
r_scangle_it2.042
r_mcangle_it1.711
r_scbond_it1.456
r_angle_refined_deg1.098
r_mcbond_it1.08
r_nbtor_refined0.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.083
r_dihedral_angle_4_deg15.638
r_dihedral_angle_3_deg15.492
r_dihedral_angle_1_deg5.566
r_scangle_it2.042
r_mcangle_it1.711
r_scbond_it1.456
r_angle_refined_deg1.098
r_mcbond_it1.08
r_nbtor_refined0.293
r_symmetry_vdw_refined0.198
r_nbd_refined0.197
r_symmetry_hbond_refined0.152
r_xyhbond_nbd_refined0.149
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.003
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 Atoms8668
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms70

Software

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