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X-ray crystal structure of SARS-CoV-2 main protease complex with Bofutrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 J852 F07_10: 0.1 M Bis-Tris propane, pH 9.0, 25% w/v PEG1500, 0.1 M sodium chloride
Crystal Properties Matthews coefficient Solvent content 1.94 36.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.156 α = 90 b = 52.593 β = 101.59 c = 46.229 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 200 PIXEL DECTRIS EIGER X 9M 2024-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.979 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.909 34.23 63.3 0.062 0.075 0.041 10.2 3.1 12730 32.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.909 2.05 16.6 0.749 0.886 0.47 3.4
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 1.91 34.23 1.34 12715 638 63.22 0.2163 0.2147 0.2146 0.2471 0.247 44.98
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 14.5427 f_angle_d 0.8756 f_chiral_restr 0.0702 f_plane_restr 0.0066 f_bond_d 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2340 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing