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Identification of Novel Allosteric Inhibitors of Hepatitis C Virus NS5B Polymerase Thumb Domain (Site II) by Structure-Based Design
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BRK PDB ENTRY 2BRK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.79 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.764 α = 90 b = 96.175 β = 90 c = 95.683 γ = 90
Symmetry Space Group P 21 21 2
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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.95 20 99.6 0.06 25 3.9 45650 3 19.4
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) 1 1.95 1.98 99.6 0.31 5 3.8
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 PDB ENTRY 2BRK 1.95 20 43553 1840 99.45 0.191 0.189 0.199 0.244 0.2498 RANDOM 19.26
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] 0.12 -1.29 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.358 r_scangle_it 2.955 r_scbond_it 1.765 r_angle_refined_deg 1.75 r_angle_other_deg 1.343 r_mcangle_it 1.267 r_mcbond_it 0.663 r_nbd_refined 0.314 r_symmetry_vdw_other 0.277 r_nbd_other 0.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.358 r_scangle_it 2.955 r_scbond_it 1.765 r_angle_refined_deg 1.75 r_angle_other_deg 1.343 r_mcangle_it 1.267 r_mcbond_it 0.663 r_nbd_refined 0.314 r_symmetry_vdw_other 0.277 r_nbd_other 0.271 r_xyhbond_nbd_refined 0.225 r_symmetry_hbond_refined 0.219 r_symmetry_vdw_refined 0.114 r_nbtor_other 0.094 r_chiral_restr 0.082 r_gen_planes_other 0.036 r_bond_refined_d 0.02 r_gen_planes_refined 0.02 r_bond_other_d 0.015 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4132 Nucleic Acid Atoms Solvent Atoms 629 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing