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Crystal structure of SAR-CoV-2 3CL protease complex with inhibitor SH-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 17.5% PEG4000
0.1M sodium acetate pH 4.6
0.2 M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.25 45.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.111 α = 90 b = 63.286 β = 90 c = 106.697 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER X 16M 2020-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.15 44.55 100 0.231 12.63 13.3 17272 21.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.27 0.971 3.47
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 6Y2F 2.15 41.55 1.36 17270 864 99.99 0.1934 0.1913 0.1919 0.2346 0.2345 22.43
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 11.0416 f_angle_d 0.956 f_chiral_restr 0.0537 f_plane_restr 0.0088 f_bond_d 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2339 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building