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X-ray structure of SARS-CoV-2 main protease M165I covalently bound to inhibitor GRL-051-22 at 1.90 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9E7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 16% PEG 10K, 0.003 M DTT, 1% MPD, 0.05 M MES (pH 6.0), 0.16 M KCl, 2.5% DMSO, 25 mM HEPES, protein concentration 5.5 mg/mL
Crystal Properties Matthews coefficient Solvent content 2.84 56.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.112 α = 90 b = 81.915 β = 117.307 c = 54.337 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 EIGER2 S 4M confocal VariMax-VHF Arc Sec optics 2025-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5406
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 1.9 18.03 99.89 0.09864 0.1095 0.04692 0.994 11.51 5.2 29825 25.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 99.81 0.7062 0.7062 0.344 0.769 1.91 5.1
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 1.9 18.03 1.35 29792 1999 99.89 0.1651 0.1615 0.163 0.2156 0.2152 34.16
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 16.0656 f_angle_d 1.0935 f_chiral_restr 0.0596 f_bond_d 0.011 f_plane_restr 0.0095
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling PHENIX phasing