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Discovery of an orally bioavailable reversible covalent SARS-CoV-2 Mpro inhibitor with pan-coronavirus activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M Magnesium sulfate heptahydrate,
Crystal Properties Matthews coefficient Solvent content 2 38.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.611 α = 90 b = 106.543 β = 102.339 c = 54.605 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315r 2021-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95365 Australian Synchrotron MX2
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 1.47 47.7 99.8 0.999 14.5 6.9 92033 16.78
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 1.47 1.49 0.811
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 6Y2G 1.47 47.49 1.38 91992 2000 99.79 0.1856 0.1851 0.1851 0.2078 0.2074 21.86
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 17.2596 f_angle_d 1.105 f_chiral_restr 0.0875 f_plane_restr 0.0074 f_bond_d 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4692 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 80
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing