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Crystal structure of SARS CoV-2 3CL protease in complex with GSK4365096A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5R7Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 295 0.1M HEPES, pH 7.5, 16% PEG8000, 0.1M KH2PO4
Crystal Properties Matthews coefficient Solvent content 2.6 52.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.724 α = 90 b = 100.404 β = 90 c = 103.116 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 EIGER2 S 16M 2021-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 2.02 100 90.1 0.122 0.135 0.057 0.986 7.3 5.3 45983 24.65
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 2.65 2.7 0.91 0.454 0.47
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 FREE R-VALUE 2.02 41.02 1.35 45981 1998 98.47 0.1895 0.1881 0.1891 0.2202 0.2204 32.08
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 6.9571 f_angle_d 0.7129 f_chiral_restr 0.0438 f_plane_restr 0.0065 f_bond_d 0.0032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4596 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 90
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing