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Crystal structure of SARS main protease in complex with Bofutrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CA8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1M Hepes pH7.5, 15% PEG8000, 10% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.1 60.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.008 α = 91.952 b = 59.787 β = 102.776 c = 67.836 γ = 108.403
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 2024-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979191 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.04 65.74 97.6 0.066 8.9 3 49399 32.0230947469
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.09 0.318
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 7CA8 2.04 26.82 1.97340568875 49298 2375 97.4731097754 0.239932071284 0.238197115643 0.2382 0.273941421456 0.2745 40.9174705953
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 7.08724348743 f_angle_d 1.02590644688 f_chiral_restr 0.0549241319847 f_bond_d 0.00799929685251 f_plane_restr 0.0069389403401
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4382 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 66
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing