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X-ray crystal structure of SARS-CoV-2 main protease triple mutants in complex with Bofutrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other D_1000279058
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 J000582,D04_00, MD ECO PACT premiet HT96 Eco: 0.1 M MMT, pH 7.0, 25% w/v PEG1500
Crystal Properties Matthews coefficient Solvent content 1.98 37.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.176 α = 90 b = 53.486 β = 102.39 c = 44.935 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 EIGER X 16M 2023-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979493 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.09 48.2 88.8 0.208 0.208 0.273 0.14 0.952 4.9 3.6 9805
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.32 45.4 1.16 1.16 1.58 0.8 0.307 3.6
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 2.09 48.15 1.35 9794 479 62.31 0.2159 0.2127 0.2126 0.2783 0.2783
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 14.201 f_angle_d 0.445 f_chiral_restr 0.059 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2330 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing