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Crystal structure of SARS main protease in complex with Ibuzatrelvir
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, SITTING DROP 298 0.1M Hepes pH7.5, 10% PEG8000, 8% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.14 60.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.257 α = 92.645 b = 60.489 β = 102.581 c = 67.906 γ = 108.672
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 2024-03-13 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) 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 56.85 97.9 0.06 11.2 3.3 50311 29.5478432815
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 0.316
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 32.75 1.9752299345 50236 2455 97.807717768 0.191800406929 0.190360679192 0.193 0.219466585345 0.2197 36.9944767996
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 5.697940216 f_angle_d 0.912830910385 f_chiral_restr 0.0532137219435 f_bond_d 0.00775142756761 f_plane_restr 0.00609641971345
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4427 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction PHENIX phasing