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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, 5 MM DTT, PH 4.7, Transferred to pH 7.6 for compound soaking and data collection, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.701 α = 90 b = 106.423 β = 90 c = 126.431 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 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2006-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 39.19 99.1 0.12 18 7.3 67661 67661 32.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.18 98.8 0.742 2.26 6.9 6662
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2.1 39.19 67597 67597 3353 99 0.22 0.22 0.218 0.2208 0.266 0.2663 RANDOM 42.557
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] -0.91 1.84 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.768 r_dihedral_angle_3_deg 14.537 r_dihedral_angle_4_deg 13.058 r_dihedral_angle_1_deg 5.608 r_scangle_it 2.43 r_mcangle_it 1.835 r_scbond_it 1.594 r_mcbond_it 1.148 r_angle_refined_deg 1.146 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.768 r_dihedral_angle_3_deg 14.537 r_dihedral_angle_4_deg 13.058 r_dihedral_angle_1_deg 5.608 r_scangle_it 2.43 r_mcangle_it 1.835 r_scbond_it 1.594 r_mcbond_it 1.148 r_angle_refined_deg 1.146 r_nbtor_refined 0.295 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.191 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.074 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 8734 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling EPMR phasing