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Crystal structure of HCV polymerase NS5b genotype 2a JFH-1 isolate with the S15G, C223H, V321I resistance mutations against the guanosine analog GS-0938 (PSI-3529238)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YUY PDB ENTRY 1YUY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 NS5b VCID 5854 at 4.25 mg/mL in 5 mM Tris pH 7.5, 200 mM NH4OAc, 1 mM EDTA 1 mM DTT against PACT screen condition D5, 25% PEG 1500, 0.1M MMT Malic Acid, MES, Tris Buffer pH 8.0 supplemented with 20% glycerol as cryo-protectant, crystal tracking ID 223572d5, puck ID cps0237-1, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 4.05 69.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.208 α = 90 b = 140.208 β = 90 c = 92.567 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 325 mm CCD 2011-06-30 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 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 2.5 50 99.7 0.085 21.9 7.8 35841
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 2.5 2.57 97.3 0.638 2.3 3.7 2877
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 1YUY 2.5 50 35745 1792 99.58 0.1899 0.1882 0.1861 0.2234 0.222 RANDOM 39.3253
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] 1.88 0.94 1.88 -2.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.85 r_dihedral_angle_3_deg 15.998 r_dihedral_angle_4_deg 14.859 r_dihedral_angle_1_deg 5.848 r_scangle_it 3.585 r_scbond_it 2.1 r_mcangle_it 1.452 r_angle_refined_deg 1.421 r_mcbond_it 0.741 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.85 r_dihedral_angle_3_deg 15.998 r_dihedral_angle_4_deg 14.859 r_dihedral_angle_1_deg 5.848 r_scangle_it 3.585 r_scbond_it 2.1 r_mcangle_it 1.452 r_angle_refined_deg 1.421 r_mcbond_it 0.741 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4277 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 43
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling