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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 NS5B 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, TRANSFERED TO PH 7.6 FOR LIGAND SOAKING, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.25 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.302 α = 90 b = 106.258 β = 90 c = 126.225 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 2006-10-31 M MAD
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 2.31 38.12 99.9 0.21 5.15 4.1 51042 51042 37.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.31 2.39 96.5 3.4 4910
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 NS5B POLYMERASE 2.31 38.12 51041 2606 98.95 0.2103 0.2103 0.20695 0.2097 0.27228 0.2695 RANDOM 47.778
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] -1.11 2.42 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.836 r_dihedral_angle_3_deg 15.301 r_dihedral_angle_4_deg 15 r_dihedral_angle_1_deg 5.543 r_scangle_it 2.425 r_mcangle_it 1.898 r_scbond_it 1.701 r_mcbond_it 1.184 r_angle_refined_deg 1.155 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.836 r_dihedral_angle_3_deg 15.301 r_dihedral_angle_4_deg 15 r_dihedral_angle_1_deg 5.543 r_scangle_it 2.425 r_mcangle_it 1.898 r_scbond_it 1.701 r_mcbond_it 1.184 r_angle_refined_deg 1.155 r_nbtor_refined 0.293 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.136 r_symmetry_hbond_refined 0.134 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 278 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling EPMR phasing