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SARS-CoV-2 Main protease bound to a non-covalent non-peptidic HTS hit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 290 0.1 M MES pH 6.8, 0.2 M lithium sulfate, 24% PEG3350
Crystal Properties Matthews coefficient Solvent content 2 38.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.146 α = 79.6 b = 54.223 β = 70.18 c = 59.906 γ = 88.46
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 PILATUS 6M 2021-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 1.75 50 93.7 0.095 0.123 0.078 0.988 5.4 2.1 48462
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 91.1 0.568 0.746 0.479 0.598 1.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.76 42.48 1.98 48444 2243 92.51 0.1652 0.1634 0.1634 0.2013 0.2013 1
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 7.857 f_angle_d 0.867 f_chiral_restr 0.057 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4706 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 155
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing