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X-ray structure of SARS-CoV-2 main protease covalently bound to inhibitor GRL-050-22 at 1.16 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 6 277 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 2.87 57.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.95 α = 90 b = 82.339 β = 117.435 c = 54.291 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 X 16M 2022-12-13 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 1.16 20.29 95.92 0.06836 0.995 8.03 2 245345 13.49
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 1.16 1.19 94.77 0.594 1.05
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 1.16 20.29 1.34 126670 1999 95.92 0.1414 0.1411 0.1606 0.1594 0.1722 24.14
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 15.2496 f_angle_d 1.2059 f_chiral_restr 0.0918 f_bond_d 0.0158 f_plane_restr 0.0105
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2368 Nucleic Acid Atoms Solvent Atoms 501 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing