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Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with PF07321332
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 21% PEG3350, 0.1M Na2SO4
Crystal Properties Matthews coefficient Solvent content 2.74 55.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.028 α = 90 b = 102.316 β = 90 c = 103.299 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 EIGER2 S 9M 2023-01-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.92 46.1 95.8 0.064 22.8 11 53681 29.9926979249
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 2.02 0.654
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 1.92 46.1 1.34354817013 53589 2000 95.6826825218 0.209573701802 0.208294553813 0.2107 0.242365627241 0.2443 35.5201640939
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 6.15234811448 f_angle_d 1.03135655669 f_chiral_restr 0.0552411817072 f_bond_d 0.00702218575461 f_plane_restr 0.00591973762642
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4530 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 70
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing