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Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the noncovalently bound inhibitor C5N17B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 295 1.5 mM inhibitor, 24% PEG1500, 0.05 M sodium malonate, 0.075 M imidazole, 0.075 M boric acid, 5 % DMSO, 1 mM DTT, 1.58 mM EDTA, 26.67 mM Tris, 20 mM NaCl, 1.33 mM TCEP, pH 7.8
Crystal Properties Matthews coefficient Solvent content 2.67 53.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.835 α = 90 b = 100.022 β = 90 c = 104.641 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2023-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.67 72.3 93.8 0.093 0.096 0.026 0.999 14.9 13.8 61110
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.8 65.1 1.626 0.454 0.611 1.5 13.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS FREE R-VALUE 1.67 40.25 61093 2992 72.85 0.1879 0.1856 0.1867 0.2327 0.233
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 14.282 f_angle_d 1.085 f_chiral_restr 0.059 f_bond_d 0.011 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4652 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling STARANISO data scaling PHENIX phasing