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Crystal structure of HCV NS3/4A protease in complex with NR01-127
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VOJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 100 mM MES Buffer pH 6.5, 4% (W/V) Ammonium Sulfate, 20-26% PEG 3350
The cryogenic condition is 100 mM MES Buffer pH 6.5, 4% (W/V) Ammonium Sulfate, 20-26% PEG 3350, 15% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.27 45.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.882 α = 90 b = 58.653 β = 90 c = 59.857 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU SATURN 944 2019-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.78 22.95 97.42 0.998 18.57 6.3 18600 12.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.884 0.939
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5VOJ 1.78 22.95 1.34 18598 940 97.5 0.1525 0.1505 0.1513 0.1895 0.19 15.01
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 f_dihedral_angle_d 7.2969 f_angle_d 1.3881 f_chiral_restr 0.072 f_bond_d 0.0122 f_plane_restr 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1400 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 95
Software Software Software Name Purpose PHENIX refinement PHASER phasing HKL-3000 data scaling Coot model building