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Crystal structure of the main protease (3CLpro/Mpro) of SARS-CoV-2 obtained in presence of 5 millimolar X77 enantiomer R.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BB2 7BB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.12 M Diethylene glycol 0.12M Triethylene
glycol 0.12M Tetraethylene glycol 0.12M
Pentaethylene glycol, 0.1 M Tris/bicine pH 8.5, 20% v/v Ethylene glycol, 10% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.6 52.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.568 α = 90 b = 100.247 β = 90 c = 103.919 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 2021-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.9718 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 1.66 103.92 99.7 0.097 0.999 14 11 83674 22.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.69 0.661
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 1.66 49.32 1.34 83577 4313 99.55 0.1669 0.1656 0.1656 0.1889 0.1885 32.55
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 13.9909 f_angle_d 1.153 f_chiral_restr 0.0568 f_plane_restr 0.01 f_bond_d 0.0094
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4687 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 115
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing