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Crystal structure of SARS main protease in complex with Ibuzatrelvir Pomotrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8YKK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1M Hepes pH7.5, 10% PEG8000, 8% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.14 60.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.115 α = 93.136 b = 60.358 β = 102.503 c = 68.168 γ = 108.54
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 2.05 65.96 97.7 0.092 8 3.1 49370 22.2404617737
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 2.05 2.1 0.494
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 2.05 28.36 1.96221741951 49159 2376 97.2809847031 0.219960902095 0.218542479212 0.2187 0.247675598658 0.2483 31.8827959844
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 7.64388538546 f_angle_d 0.993465051953 f_chiral_restr 0.0585912994534 f_bond_d 0.00750281984587 f_plane_restr 0.00617522888538
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4434 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing