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Structure of the genotype 2B HCV polymerase bound to a NNI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GSZ PDB ENTRY 3GSZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 300 10% PEG4000, 0.1M sodium citrate, 0.2M sodium chloride, 5mM DTT, Protein concentration 6.5mg/ml, pH6.1, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.293 α = 90 b = 64.648 β = 89.73 c = 135.714 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 4 2005-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 20 98 0.091 10.5 3.3 88994 88994 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 93.7 0.511 2.2 3.1 8472
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 (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 3GSZ 2 19.84 88500 88500 4442 100 0.18353 0.18168 0.1916 0.21823 0.2283 RANDOM 22.227
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] -0.74 0.91 0.32 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.613 r_scangle_it 3.072 r_scbond_it 1.782 r_angle_refined_deg 1.208 r_mcangle_it 1.142 r_angle_other_deg 0.902 r_mcbond_it 0.592 r_symmetry_vdw_other 0.256 r_symmetry_hbond_refined 0.235 r_nbd_other 0.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.613 r_scangle_it 3.072 r_scbond_it 1.782 r_angle_refined_deg 1.208 r_mcangle_it 1.142 r_angle_other_deg 0.902 r_mcbond_it 0.592 r_symmetry_vdw_other 0.256 r_symmetry_hbond_refined 0.235 r_nbd_other 0.231 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.151 r_nbtor_other 0.08 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8749 Nucleic Acid Atoms Solvent Atoms 851 Heterogen Atoms 52
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling