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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) F140L Mutant in Complex with Inhibitor Nirmatrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VH8 7VH8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293 0.05% w/v (-)-Menthol, 0.05% w/v Caffeic acid, 0.05% w/v D-Quinic acid, 0.05% w/v Shikimic acid, 0.05% w/v Gallic acidmonohydrate, 0.05% w/v N-Vanillylnonanamide, 0.05% w/v Thymol, 0.1 M Buffer System 2 pH 7.5 (sodium HEPES, MOPS acid), 20% v/v ethylene glycol, 10% w/v PEG 8,000
Crystal Properties Matthews coefficient Solvent content 2.3 46.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.965 α = 90 b = 64.457 β = 90 c = 105.116 γ = 90
Symmetry Space Group P 21 21 2
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 2022-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.953740 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.25 27.87 99.6 0.086 0.09 0.999 18.95 13.047 15428 47.13
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.38 99.1 0.797 0.829 0.88 3.3 13.187
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 7VH8 2.25 27.87 1.36 15410 1540 99.75 0.21 0.2057 0.2069 0.2476 0.2484 51.8503
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2351 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 35
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction autoPROC data reduction PHENIX phasing