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Crystal Structure of HCV NS5B Polymerase with a Novel Pyridazinone Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other HCV POLYMERASE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 298 20% PEG 4K, 50 mM ammonium sulfate, 100 mM sodium acetate pH 4.7, 5 mM DTT. Transferred to pH 7.6 for soaking., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.17 43.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.536 α = 90 b = 103.905 β = 90 c = 125.932 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2006-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 41.9 95.7 48377 48377
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT HCV POLYMERASE 2.3 41.88 48337 2394 95.7 0.244 0.244 0.242 0.239 0.299 0.2928 RANDOM 38.183
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] -3.5 8.53 -5.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.532 r_dihedral_angle_3_deg 15.681 r_dihedral_angle_4_deg 14.982 r_dihedral_angle_1_deg 5.606 r_scangle_it 1.977 r_scbond_it 1.25 r_angle_refined_deg 1.151 r_mcangle_it 0.953 r_mcbond_it 0.549 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.532 r_dihedral_angle_3_deg 15.681 r_dihedral_angle_4_deg 14.982 r_dihedral_angle_1_deg 5.606 r_scangle_it 1.977 r_scbond_it 1.25 r_angle_refined_deg 1.151 r_mcangle_it 0.953 r_mcbond_it 0.549 r_nbtor_refined 0.309 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.204 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 Atoms Number Protein Atoms 8668 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing