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SARS-CoV-2 Mpro in complex with compound 6k inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291.15 0.2 M Ammonium sulfate, 25% w/v Polyethylene glycol 3,350, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.04 39.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.743 α = 90 b = 53.776 β = 101.98 c = 45.409 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 PIXEL DECTRIS EIGER2 X 16M 2022-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.14 55.56 99.4 0.09 0.043 0.997 9.9 5.3 14979 47.78
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 2.14 2.2 99.3 1.459 0.722 0.388 1 4.9
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.31 48.58 1.38 11939 1194 98.09 0.1977 0.194 0.1938 0.2309 0.2318 56.97
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 8.4061 f_angle_d 0.4589 f_chiral_restr 0.0403 f_plane_restr 0.0048 f_bond_d 0.0019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2327 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing