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Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor PSB-21110 (compound 29b in publication)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7L5D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 1.0 M imidazole/MES (pH 6.5), 0.3 M NaF, 0.3 M NaBr, 0.3 M NaI; 30% (v/v), 12% (v/v) PEG500 MME, 6% (w/v) PEG20000
Crystal Properties Matthews coefficient Solvent content 2.75 55.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.501 α = 90 b = 81.584 β = 114.82 c = 51.589 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M 2022-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9762 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.25 46.82 49.1 0.051 0.999 15.6 6.3 51602 16.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.43 0.844 0.696 1.8
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 FOURIER SYNTHESIS FREE R-VALUE 1.25 46.82 1.36 51602 2589 51.32 0.1829 0.1813 0.1814 0.2135 0.2138
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 12.003 f_angle_d 0.916 f_chiral_restr 0.077 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2322 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 13
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALEPACK data scaling PHENIX phasing