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Crystal structure of a product state assembly of HCV NS5B genotype 2a JFH-1 isolate with beta hairpin deletion bound to primer-template RNA with a 2',3'-ddC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E76 PDB ENTRY 4E76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 4.37 mg/mL NS5B in 20 mM Tris, pH 8, 200 mM sodium chloride, 20% glycerol, 2 mM TCEP, 200 mM imidazole against 30% PEG3350, 0.1 M Bis-Tris propane, pH 6.0, 200 mM ammonium acetate soaked overnight in precipitant supplemented with 15% ethylene glycol as cryoprotectant and 0.2 mM CUAGGC(DOC), crystal tracking ID 228018H11, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.95 68.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.73 α = 90 b = 142.73 β = 90 c = 91.5 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 2011-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 3 50 99.5 0.099 16.76 5.3 21395 21289 -3 59.238
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 3 3.08 99.6 0.745 2.27
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 4E76 3 50 21288 1093 99.5 0.197 0.194 0.1993 0.241 0.2408 RANDOM 55.3872
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] 2.5 1.25 2.5 -3.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.612 r_dihedral_angle_3_deg 17.484 r_dihedral_angle_4_deg 13.772 r_dihedral_angle_1_deg 6.125 r_angle_refined_deg 1.34 r_angle_other_deg 0.899 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.612 r_dihedral_angle_3_deg 17.484 r_dihedral_angle_4_deg 13.772 r_dihedral_angle_1_deg 6.125 r_angle_refined_deg 1.34 r_angle_other_deg 0.899 r_chiral_restr 0.069 r_bond_refined_d 0.009 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_mcbond_it r_mcbond_other r_mcangle_it 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 4038 Nucleic Acid Atoms 197 Solvent Atoms 18 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction