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Crystal structure of SARS-Cov-2 main protease in complex with Leritrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9JGR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1M HEPES 7.5, 20% PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.43 49.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.25 α = 90 b = 90.91 β = 90 c = 102.37 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 2024-09-13 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) 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 1.76 51.19 98.9 0.992 11.3 11.1 63014 12.4711754877
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 1.76 1.81 0.599
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 1.76 51.19 1.32796731856 62891 3120 98.5597868673 0.22178787454 0.220002797844 0.2202 0.255210423733 0.2549 21.4695480557
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 7.72812206905 f_angle_d 1.26289382706 f_chiral_restr 0.0777969876544 f_bond_d 0.00844362045677 f_plane_restr 0.00665903077759
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4495 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 90
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing