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HCV NS3-4a protease domain with a ketoamide inhibitor derivative of Boceprevir bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O8M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 uL protein solution mixed with 4 uL (0.75-1.00) M NaCl, 0.1 M MES, 0.1 M Na/K PO4, pH 5.6-6.2, suspended over 1 mL reservoir solutions of (1.25-1.50) M NaCl, 0.1 M MES, 0.1 M Na/K PO4, 5 mM beta-mercaptoethanol, pH 5.6-6.2. The trays were set at 4C for 5-7 days to control nucleation, followed by incubation for 3 weeks at 12C to maximize crystal growth, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.84 68.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 224.02 α = 90 b = 224.02 β = 90 c = 75.24 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 IMAGE PLATE RIGAKU RAXIS IV 2001-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.65 50 99 21990 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.77 99 21990
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB Entry 208M 2.65 8 1 22189 18454 1823 83.2 0.19 0.2017 0.273 0.2859 Random
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]
RMS Deviations Key Refinement Restraint Deviation x_angle_d 1.903 x_improper_angle_d 1.306 x_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2724 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 46
Software Software Software Name Purpose HKL-2000 data collection X-PLOR model building X-PLOR refinement HKL-2000 data reduction SCALEPACK data scaling X-PLOR phasing