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Crystal structure of SU3327 (halicin) covalently bound to the main protease (3CLpro/Mpro) of SARS-CoV-2.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.09M NPS (Sodium nitrate, Sodium phosphate dibasic, Ammonium sulfate), 0.1M Hepes/Mops pH 7.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.62 52.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.234 α = 90 b = 100.015 β = 90 c = 103.698 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 PILATUS 6M 2021-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00000 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.93 103.7 99.8 0.107 0.998 11 6.3 53997 28.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.98 1.295 0.609
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 7BB2 1.93 46.03 1.34 53915 2766 99.72 0.1756 0.1744 0.1812 0.1982 0.2043 38.76
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 13.5581 f_angle_d 0.6968 f_chiral_restr 0.0444 f_plane_restr 0.0062 f_bond_d 0.0039
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4627 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 84
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing