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Crystal structure of SARS-CoV-2 3CLpro S301P mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EN8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 293 0.2 M BIS-TRIS, pH 6.6, 20% polyethylene glycol 4,000
Crystal Properties Matthews coefficient Solvent content 1.96 37.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.619 α = 90 b = 53.404 β = 100.529 c = 113.384 γ = 90
Symmetry Space Group I 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 RIGAKU HyPix-6000HE 2021-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.541
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 27.87 99.65 0.08929 0.1006 0.04548 0.996 14.69 4.9 17820 24.66
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 2 2.072 99.6 0.3017 0.3394 0.1533 0.906 3.85 4.7
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 27.87 1.34 17819 1782 99.69 0.1848 0.1792 0.1795 0.2352 0.2371 28.87
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 6.6809 f_angle_d 0.9354 f_chiral_restr 0.0514 f_bond_d 0.0078 f_plane_restr 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2341 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms
Software Software Software Name Purpose CrysalisPro data collection PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling PHENIX phasing