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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, transferred to pH 7.6 for soaking, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.637 α = 90 b = 106.258 β = 90 c = 126.93 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 2006-03-27 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 37.9 99.9 0.098 21.2 7.1 68398 68398 28.7
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) 2.1 2.18 100 0.53 3.4 6.9 6722
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 (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 37.9 68328 3520 99.89 0.19248 0.19053 0.1957 0.22786 0.2269 RANDOM 34.537
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] -0.02 0.75 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.1 r_dihedral_angle_4_deg 14.532 r_dihedral_angle_3_deg 13.127 r_dihedral_angle_1_deg 5.313 r_scangle_it 2.539 r_mcangle_it 1.786 r_scbond_it 1.744 r_mcbond_it 1.173 r_angle_refined_deg 1.06 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.1 r_dihedral_angle_4_deg 14.532 r_dihedral_angle_3_deg 13.127 r_dihedral_angle_1_deg 5.313 r_scangle_it 2.539 r_mcangle_it 1.786 r_scbond_it 1.744 r_mcbond_it 1.173 r_angle_refined_deg 1.06 r_nbtor_refined 0.294 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.187 r_symmetry_hbond_refined 0.134 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 Atoms Number Protein Atoms 8670 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling EPMR phasing