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HCV NS5B polymerase genotype 1b in complex with 1,5 benzodiazepine 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NB4 PDB ENTRY 1NB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.75 293 5-8% PEG 6000, 100mM Mg-Salts, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.91 57.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.274 α = 90 b = 107.679 β = 90 c = 133.573 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 PIXEL PSI PILATUS 6M 2008-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0073 SLS X06SA
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 1.9 44.9 99.9 0.086 6.5 120846 120846
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 1.9 1.95 100 0.18 6.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NB4 1.9 44.9 119878 119878 967 100 0.18423 0.18423 0.18403 0.20861 0.2909 RANDOM 42.899
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] 2.78 -0.94 -1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.946 r_dihedral_angle_4_deg 14.812 r_dihedral_angle_3_deg 12.76 r_scangle_it 6.328 r_dihedral_angle_1_deg 5.574 r_scbond_it 4.83 r_mcangle_it 3.075 r_mcbond_it 2.657 r_angle_refined_deg 1.319 r_angle_other_deg 0.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.946 r_dihedral_angle_4_deg 14.812 r_dihedral_angle_3_deg 12.76 r_scangle_it 6.328 r_dihedral_angle_1_deg 5.574 r_scbond_it 4.83 r_mcangle_it 3.075 r_mcbond_it 2.657 r_angle_refined_deg 1.319 r_angle_other_deg 0.781 r_mcbond_other 0.673 r_symmetry_vdw_other 0.242 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.202 r_nbd_other 0.179 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.146 r_nbtor_other 0.084 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 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 8752 Nucleic Acid Atoms Solvent Atoms 672 Heterogen Atoms 124
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling