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Structure of SARS-CoV main protease bound to potent broad-spectrum non-covalent inhibitor X77
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 278 3 uL drops that were formed by adding 1 uL of purified SARS-3CLpro (10 mg/mL) that had been incubated for three hours with a 3 molar excess of the of compound X77, and 2 uL of reservoir solution: 3 mM DTT, 50 mM MES pH 6.0, 40 mM KCl, 1% MPD, and 5% PEG-10K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.881 α = 90 b = 81.26 β = 104.231 c = 53.455 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 CCD MARMOSAIC 300 mm CCD 2020-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.978 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.46 100 99.7 0.049 0.022 41.3 4.9 77810 18.31
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.46 1.49 99.7 0.62 0.286 0.908 2.6 4.5
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 FREE R-VALUE 4MDS 1.46 32.28 1.37 77771 2000 99.5 0.157 0.1564 0.1564 0.1773 0.177 30.07
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 19.2604 f_angle_d 0.8978 f_chiral_restr 0.078 f_plane_restr 0.0056 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHENIX phasing