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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) G15S 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 1%(2% w/v Cytidine, 2% w/v Inosine, 2% w/v Ribavirin, 2% w/v Thymidine, 2% w/v Uridine), 0.1M(Sodium HEPES; MOPS (acid))PH7.5, 30%(40% v/v PEG 500* MME; 20 % w/v PEG 20000)
Crystal Properties Matthews coefficient Solvent content 2.72 54.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.507 α = 90 b = 80.562 β = 114.51 c = 51.548 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 1.77 29.44 99.5 0.07400000000000001 0.08 0.9990000000000001 13.6 6.9 35266
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 1.77 1.88 0.879 0.951 0.847
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 1.77 29.44 1.35 35230 1998 99.68 0.1957 0.1941 0.1945 0.2208 0.2222
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 6.066 f_angle_d 0.97 f_chiral_restr 0.056 f_plane_restr 0.01 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2312 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement autoPROC data reduction PHENIX phasing