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Crystal structure of SARS-Cov-2 main protease H163A mutant in complex with Pomotrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YRZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1M Na2SO4,24% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.68 54.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.147 α = 90 b = 101.989 β = 90 c = 102.152 γ = 90
Symmetry Space Group P 21 21 21
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 2024-06-15 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 1.98 102.15 99.5 0.116 6 11.4 49291 21.8119803037
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 1.98 2.03 0.647
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 1.98 72.17 1.34063656695 49166 2466 99.2030023607 0.191256776983 0.189287755158 0.195 0.229568181913 0.2311 25.3361683427
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 6.39948224869 f_angle_d 0.907953623084 f_chiral_restr 0.0518873300527 f_bond_d 0.00695172558515 f_plane_restr 0.00565602623979
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4484 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing