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Structure of HCV NS3-4A Protease with an Inhibitor Derived from a Boronic Acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O8M HCV NS3(1-181)S139A - NS4a pdb2o8m.ent
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 Crystallization was performed by the vapor diffusion method using hanging drops (4 L protein solution mixed with 4 L (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 -mercaptoethanol, pH 5.6-6.2. The trays were set at 4oC for 5-7 days to control nucleation, followed by incubation for 3 weeks at 12oC to maximize crystal growth., VAPOR DIFFUSION, HANGING DROP, temperature 277, then 285K
Crystal Properties Matthews coefficient Solvent content 3.89 68.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 224.483 α = 90 b = 224.483 β = 90 c = 75.786 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 ADSC QUANTUM 210 2004-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
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 2.15 50 71.6 0.075 13.5 2.8 39911 28576 1
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) 2.15 2.2 20.6 0.288 2 2631
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 HCV NS3(1-181)S139A - NS4a
pdb2o8m.ent 2.3 8 1 25697 20909 2089 0.18 0.1918 0.256 0.1849 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 c_angle_deg 2.019 c_improper_angle_d 1.476 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2727 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 45
Software Software Software Name Purpose ADSC data collection X-PLOR model building X-PLOR refinement HKL-2000 data reduction SCALEPACK data scaling X-PLOR phasing