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Crystal structure of the main protease (3CLpro/Mpro) of SARS-CoV-2 obtained in presence of 75 micromolar X77.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BB2 7BB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M DL-Glutamic acid monohydrate, 0.1M
DL-Alanine 0.1M Glycine 0.1M DL-Lysine
monohydrochloride 0.1M DL-Serine, 0.1M Hepes/MOPS pH 7.5, 20% v/v Ethylene glycol 10 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.64 53.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.66 α = 90 b = 100.829 β = 90 c = 104.647 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 PIXEL DECTRIS PILATUS 6M 2021-05-12 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 1.6 104.65 100 0.124 0.997 9.8 8.8 95019 20.08
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 1.6 1.63 0.581
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 7BB2 1.6 49.5 1.34 94917 4838 99.98 0.1683 0.1675 0.1676 0.1833 0.1837 28.49
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 14.0673 f_angle_d 1.1243 f_chiral_restr 0.061 f_bond_d 0.0088 f_plane_restr 0.0083
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4726 Nucleic Acid Atoms Solvent Atoms 625 Heterogen Atoms 69
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing