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Crystal Structure of the SARS-CoV-2 Main Protease in Complex with Compound 61
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, SITTING DROP 8.5 294 10% v/v 2-Propanol
0.1 M BICINE pH 8.5
30% w/v Polyethylene glycol 1500
Crystal Properties Matthews coefficient Solvent content 2.62 52.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.91 α = 90 b = 99.895 β = 90 c = 104.314 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 EIGER X 16M 2021-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.3 56.91 99.55 0.1552 0.1615 0.04414 0.999 13.7 13.2 31931 53.64
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 2.3 2.38 99.18 0.6139 0.488 1.25 12.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.3 56.91 1.31 31931 2991 99.52 0.2051 0.2035 0.2038 0.2363 0.235 55.54
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 14.1166 f_angle_d 0.8851 f_chiral_restr 0.0493 f_bond_d 0.0076 f_plane_restr 0.0074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4413 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing