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Crystal structure of MG-132 covalently bound to the main protease (3CLpro/Mpro) of SARS-CoV-2 in spacegroup P1.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BBE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.05M Magnesium chloride hexahydrate , 0.1M MES pH 6.5, 5 % w/vPEG 4000, 10% v/v 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.04 39.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.282 α = 114.649 b = 54.918 β = 99.955 c = 59.503 γ = 90.536
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2021-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.9999 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 53.05 96.6 0.071 0.998 10.4 3.4 47488 23.18
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 1.8 1.84 0.566
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 7BBE 1.8 49.71 1.96 47474 2412 96.62 0.1805 0.1787 0.1785 0.2147 0.214 31.37
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 14.0569 f_angle_d 0.9437 f_chiral_restr 0.0582 f_bond_d 0.0106 f_plane_restr 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4701 Nucleic Acid Atoms Solvent Atoms 386 Heterogen Atoms 69
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing