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Crystal structure of SARS-Cov-2 main protease E166R mutant 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, SITTING DROP 298 0.1M HEPES pH6.5, 10% isopropanol, 22% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.74 55.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.319 α = 80.494 b = 60.522 β = 67.906 c = 63.152 γ = 70.402
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 2024-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979183 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 58.46 97.6 0.115 5.7 3.1 44405 24.5409823533
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 0.619
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 2.04 56.96 1.96350396737 44210 2266 97.2011520788 0.211321016228 0.208868896081 0.2183 0.255768334195 0.2517 34.6771556807
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 12.4627509459 f_angle_d 0.925342387155 f_chiral_restr 0.0502951938571 f_bond_d 0.00742694396707 f_plane_restr 0.00599821254111
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4717 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing