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Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with PF00835231
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VLP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20~24%PEG3350,0.12~0.21M sodium sulfate
Crystal Properties Matthews coefficient Solvent content 2.35 47.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.569 α = 90 b = 99.023 β = 108.49 c = 59.538 γ = 90
Symmetry Space Group P 1 21 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 2022-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
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 1.79 56.46 86 0.052 19.4 6.1 49430 26.6869872645
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 1.79 1.89 0.686
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 1.79 52.7004738108 1.35551891922 49378 2356 85.8717957636 0.199261931694 0.197804152673 0.1995 0.228327202348 0.2305 31.0268302099
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 8.22199990937 f_angle_d 0.862308294146 f_chiral_restr 0.0521958011233 f_bond_d 0.00639284957427 f_plane_restr 0.00587399989016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4439 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 68
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing