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Room-temperature X-ray Crystal structure of SARS-CoV-2 main protease in complex with Boceprevir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WQF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 287.15 18-22% PEG3350, 0.1 M Bis-Tris pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.03 39.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.277 α = 90 b = 53.407 β = 100.944 c = 113.204 γ = 90
Symmetry Space Group I 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 293 PIXEL DECTRIS EIGER R 4M 2020-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.2 27.79 99.9 0.094 0.993 9.2 4.4 13886 32.01
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 99.8 0.649 0.424 1.5 3.9
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 6WQF 2.2 27.79 1.34 13869 708 99.77 0.1791 0.176 0.1768 0.2338 0.2337 35.57
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 17.7168 f_angle_d 1.0636 f_chiral_restr 0.0625 f_bond_d 0.0079 f_plane_restr 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing