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X-ray structure of SARS-CoV-2 main protease V186I 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 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 2.24 45.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.824 α = 90 b = 62.98 β = 90 c = 104.987 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 PIXEL DECTRIS EIGER2 S 4M confocal VariMax-VHP Arc Sec optics 2024-06-12 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 21.42 99.72 0.1095 0.1202 0.04832 0.997 13.01 5.8 24595 19.69
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 1.98 99.78 0.6711 0.7531 0.3323 0.685 2.03 4.8
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 MOLECULAR REPLACEMENT FREE R-VALUE 1.9 21.42 1.34 24588 1228 99.71 0.1798 0.1774 0.1775 0.224 0.224 22.98
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 16.0894 f_angle_d 1.1166 f_chiral_restr 0.0587 f_bond_d 0.0111 f_plane_restr 0.0099
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2368 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 38
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling PHENIX phasing