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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor ensitrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HBK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293 1.2%(3% w/v CHAPS, 3% w/v CHAPSO, 3% w/v Sodium glycocholate hydrate, 3% w/v Taurocholic acid sodium salt hydrate), 0.1M(Imidazole; MES monohydrate (acid))PH6.5, 30%(40% v/v PEG 500* MME; 20 % w/v PEG 20000)
Crystal Properties Matthews coefficient Solvent content 2.73 54.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.351 α = 90 b = 82.076 β = 114.7 c = 51.476 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 2023-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.953740 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.59 29.3 99.5 0.042 0.045 0.9990000000000001 20 6.9 49187
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.68 0.5379999999999999 0.581 0.943
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 NONE 1.59 29.3 1.34 49155 1999 99.66 0.1919 0.191 0.191 0.2148 0.2144
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 8.349 f_angle_d 0.904 f_chiral_restr 0.051 f_plane_restr 0.015 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2324 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 37
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement autoPROC data reduction PHENIX phasing