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CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH S15G E86Q E87Q C223H V321I MUTATIONS IN COMPLEX WITH RNA TEMPLATE 5'-UAGG, RNA PRIMER 5'-PCC, MN2+, AND UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OBC PDB entry 4OBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 289 NS5B AT 4.7 MG/ML IN 5 MM TRIS PH 7.5, 200 MM NH4OAC, 1 MM EDTA, 1 MM DTT AGAINST 25% PEG 550 MME, 50 MM MGCL2, 0.1 M HEPES PH 7.5 FOR CRYSTAL GROWTH SOAKED INTO 28% PEG 550 MME, 0.2 M AMMONIUM ACETATE, 0.05 M BISTRIS PROPANE PH 6.0, 0.05 M TRIS PH 7.2, 12 MM MNCL2, 20 MM UDP, 4 MM 5'-UAGG, 4 MM 5'-PCC, WITH 8% GLYCEROL AS CRYO-PROTECTANT, CRYSTAL TRACKING ID 247392A4, UNIQUE PUCK ID NRC3-7
Crystal Properties Matthews coefficient Solvent content 4 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.37 α = 90 b = 140.37 β = 90 c = 92.43 γ = 120
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 300 mm CCD 2013-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.15 50 99.9 0.055 0.059 25.07 8 56292 -3 44.09
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 99.9 0.492 0.029 4.1 8.1
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 4OBC 2.15 45.99 56291 2856 99.91 0.186 0.185 0.1921 0.216 0.2235 RANDOM 41.44
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] 0.8 0.8 0.8 -2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.08 r_dihedral_angle_4_deg 14.358 r_dihedral_angle_3_deg 14.188 r_dihedral_angle_1_deg 5.826 r_mcangle_it 3.981 r_mcbond_it 2.737 r_mcbond_other 2.736 r_angle_refined_deg 1.461 r_angle_other_deg 0.79 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.08 r_dihedral_angle_4_deg 14.358 r_dihedral_angle_3_deg 14.188 r_dihedral_angle_1_deg 5.826 r_mcangle_it 3.981 r_mcbond_it 2.737 r_mcbond_other 2.736 r_angle_refined_deg 1.461 r_angle_other_deg 0.79 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4230 Nucleic Acid Atoms 110 Solvent Atoms 271 Heterogen Atoms 70
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing