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Crystal structure of ebselen covalently bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.12M alcohols (1,6-Hexanediol; 1-Butanol; 1,2-Propanediol; 2-Propanol; 1,4-Butanediol; 1,3-Propanediol), 0.1M Hepes/MOPS pH 7.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.63 53.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.739 α = 90 b = 100.455 β = 90 c = 104.597 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 2020-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.9719 ELETTRA 11.2C
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 2.05 72.45 99.8 0.086 12.3 3.7 91004 38.78
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) 1 2.05 2.11 1.264
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 2.05 52.3 1.33 86323 4226 99.83 0.1846 0.1838 0.1857 0.1991 0.2053 55.64
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 13.918 f_angle_d 0.6777 f_chiral_restr 0.0437 f_plane_restr 0.0059 f_bond_d 0.0039
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4687 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing