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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 7.4 298 20% PEG 4K, 50 mM ammonium sulfate, 100 mM sodium acetate, 5 mM DTT, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.502 α = 90 b = 104.311 β = 90 c = 125.693 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 2005-09-08 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 2.3 28.6 90.5 0.081 18 4.9 45268 45268 34.7
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) 2.3 2.38 78 0.436 3.3 4.5 3826
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 2.3 28.6 45268 45268 2286 90.51 0.195 0.195 0.192 0.1953 0.251 0.2507 RANDOM 44.129
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] -0.77 1.54 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.645 r_dihedral_angle_4_deg 15.543 r_dihedral_angle_3_deg 15.3 r_dihedral_angle_1_deg 6.177 r_scangle_it 3.347 r_scbond_it 2.094 r_angle_refined_deg 1.401 r_mcangle_it 1.357 r_mcbond_it 0.787 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.645 r_dihedral_angle_4_deg 15.543 r_dihedral_angle_3_deg 15.3 r_dihedral_angle_1_deg 6.177 r_scangle_it 3.347 r_scbond_it 2.094 r_angle_refined_deg 1.401 r_mcangle_it 1.357 r_mcbond_it 0.787 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.177 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 422 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling EPMR phasing