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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) K90R Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293 0.6%(1% w/v Ampicillin sodium salt, 1% w/v Apramycin sulfate salt, 1% w/v Bacitracin, 1% w/v Dihydrostreptomycin sesquisulfate, 1% w/v Gentamicin sulfate, 1% w/v Spectinomycin dihydrochloride pentahydrate), 0.1M(Tris (base); BICINE)PH8,5, 30%(40% v/v PEG 500* MME; 20 % w/v PEG 20000)
Crystal Properties Matthews coefficient Solvent content 2.71 54.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.118 α = 90 b = 81.021 β = 114.92 c = 51.486 γ = 90
Symmetry Space Group C 1 2 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 X 16M 2023-03-04 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 1.66 29.41 99.6 0.044000000000000004 0.048 1 18.77 6.9 42299
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 1.66 1.77 0.8079999999999999 0.873 0.8590000000000001
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 NONE 1.66 29.41 1.36 42267 1999 99.83 0.2015 0.2004 0.2004 0.2242 0.224
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 6.466 f_angle_d 0.893 f_chiral_restr 0.052 f_plane_restr 0.017 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2312 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement autoPROC data reduction PHENIX phasing