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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Enstrelvir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VU6 7VU6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.3% w/v Sodium-L ascorbate, 0.3% w/v Choline Chloride, 0.3% v/v D-Panthenol, 0.3% w/v Pyridoxine hydrochloride, 0.3% w/v Thiamine hydrochloride
20% v/v PEG 500* MME; 10% w/v PEG 20000;
0.1 M 0.1 M Buffer System 2 pH 7.5 (sodium HEPES, MOPS acid)
Crystal Properties Matthews coefficient Solvent content 2.28 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.543 α = 90 b = 98.875 β = 108 c = 58.991 γ = 90
Symmetry Space Group P 1 21 1
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 S 9M 2022-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.978642 SSRF BL02U1
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 1.8 52.83 97.4 0.079 0.085 0.999 15.29 6.912 54655 25.55
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 1.8 1.91 95.8 0.788 0.854 0.833 2.35 6.451
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7VU6 1.8 52.83 1.36 54633 1995 97.48 0.1693 0.1681 0.2013 0.1942 30.5487
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 4617 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 97
Software Software Software Name Purpose XDS data scaling PHENIX refinement PHENIX phasing