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Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalent inhibitor GUE-3642 (compound 1 in publication)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UJ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, 0.1 M HEPES and MOPS, 12 % PEG500MME, 6% PEG20000, 200 microM inhibitor, condition MORPHEUS B5
Crystal Properties Matthews coefficient Solvent content 2.58 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.006 α = 90 b = 98.647 β = 104.42 c = 67.525 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 PIXEL DECTRIS EIGER X 16M 2023-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97625 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.77 54.51 92.2 0.082 0.089 0.034 0.998 12.4 7 39350 26.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 2 64.8 1.013 0.404 0.672 1.8 7.2
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 1.77 54.51 1.35 39347 1999 59.05 0.1964 0.194 0.1941 0.2391 0.2384
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 13.596 f_angle_d 0.843 f_chiral_restr 0.05 f_plane_restr 0.017 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4642 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 99
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHENIX phasing