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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'-ACGG, RNA PRIMER 5'-PCC, MN2+, AND GDP
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, 6 MM MNCL2, 10 MM GDP, 2 MM 5'-ACGG, 2 MM 5'-PCC, WITH 8% GLYCEROL AS CRYO-PROTECTANT, CRYSTAL TRACKING ID 251148A1, UNIQUE PUCK ID HDW8-2
Crystal Properties Matthews coefficient Solvent content 4.1 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.15 α = 90 b = 140.15 β = 90 c = 92.76 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 2013-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-ID-G
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 2.8 50 99.7 0.076 0.083 19.4 6.1 25574 -3 59.52
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 2.8 2.87 99.9 0.695 0.028 2.5 6.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4OBC 2.8 50 25574 1303 99.72 0.184 0.181 0.234 0.2055 RANDOM 61.5
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] 1.77 0.88 1.77 -5.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.556 r_dihedral_angle_3_deg 16.493 r_dihedral_angle_4_deg 14.625 r_dihedral_angle_1_deg 6.035 r_mcangle_it 5.126 r_mcbond_it 3.34 r_mcbond_other 3.335 r_angle_refined_deg 1.38 r_angle_other_deg 0.968 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.556 r_dihedral_angle_3_deg 16.493 r_dihedral_angle_4_deg 14.625 r_dihedral_angle_1_deg 6.035 r_mcangle_it 5.126 r_mcbond_it 3.34 r_mcbond_other 3.335 r_angle_refined_deg 1.38 r_angle_other_deg 0.968 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 4219 Nucleic Acid Atoms 108 Solvent Atoms 62 Heterogen Atoms 92
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing