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Hepatitis C virus polymerase NS5B (BK 1-570) with HCV-796 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GIQ pdb entry 2GIQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.9 293 50 mM Na Citrate, 7.5% glycerol, 24% PEG 4000, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.287 α = 90 b = 106.2 β = 90 c = 125.94 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 MARMOSAIC 325 mm CCD 2008-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 50 94 13.4 10.7 4.9 59410 55845 28.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 91.8 68.9 1.7 3.6 5438
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 pdb entry 2GIQ 2.2 48.91 59410 52687 2782 93.37 0.21205 0.21205 0.20927 0.2133 0.26422 0.267 RANDOM 21.969
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] -0.41 1.53 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.134 r_dihedral_angle_3_deg 14.05 r_dihedral_angle_4_deg 13.962 r_dihedral_angle_1_deg 5.887 r_scangle_it 2.072 r_scbond_it 1.337 r_angle_refined_deg 1.211 r_mcangle_it 0.998 r_angle_other_deg 0.875 r_mcbond_it 0.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.134 r_dihedral_angle_3_deg 14.05 r_dihedral_angle_4_deg 13.962 r_dihedral_angle_1_deg 5.887 r_scangle_it 2.072 r_scbond_it 1.337 r_angle_refined_deg 1.211 r_mcangle_it 0.998 r_angle_other_deg 0.875 r_mcbond_it 0.601 r_symmetry_vdw_refined 0.249 r_symmetry_vdw_other 0.236 r_nbd_refined 0.194 r_nbd_other 0.188 r_symmetry_hbond_refined 0.183 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.17 r_mcbond_other 0.099 r_nbtor_other 0.084 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8766 Nucleic Acid Atoms Solvent Atoms 539 Heterogen Atoms 62
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling