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X-ray structure of SARS-CoV-2 main protease covalently bound to inhibitor GRL-062-22 at 1.65 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8UND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 12% PEG 10K, 0.003 M DTT, 1% MPD, 0.05 M MES (pH 6.0), 0.12 M KCl, 2.5% DMSO, 25 mM HEPES, protein concentration 5.5 mg/mL
Crystal Properties Matthews coefficient Solvent content 2.27 45.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.958 α = 90 b = 63.229 β = 90 c = 105.517 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2023-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.65 30.74 98.56 0.07661 0.998 12.07 4.8 70182 20.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.7 95.4 0.748 1.65
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 1.65 30.74 1.35 37086 1854 98.56 0.1609 0.159 0.1594 0.1956 0.1954 27.59
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 15.9767 f_angle_d 1.0669 f_chiral_restr 0.0625 f_bond_d 0.0089 f_plane_restr 0.0089
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing