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Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor PSB-21101 (compound 30b 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 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 2.76 55.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.534 α = 90 b = 81.215 β = 114.69 c = 51.57 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 2022-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.47 46.86 51.5 0.073 0.998 13 6.6 33735
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 1.47 1.71 0.957 0.605 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 1.47 46.86 1.35 33735 1688 54.67 0.2051 0.2032 0.2036 0.2415 0.2402
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 11.411 f_angle_d 0.576 f_chiral_restr 0.059 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2281 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 19
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHENIX phasing