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Crystal structure of SARS-Cov-2 main protease in complex with inhibitor YH-53
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7C2Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M HEPES 7.5, 20% PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.38 48.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.559 α = 90 b = 99.438 β = 107.925 c = 59.666 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 9M 2022-03-12 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 1.93 52.86 98.9 0.057 8.1 5.5 46180 28.7934372147
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 1.93 2.03 0.494
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 7C2Q 1.93 52.86 1.33933280431 46141 3858 96.6896551724 0.201372523412 0.199558744837 0.2031 0.243068261745 0.2395 33.9327775583
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 9.42365513682 f_angle_d 0.952414265572 f_chiral_restr 0.0593258663934 f_bond_d 0.00721583714591 f_plane_restr 0.00638551461785
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4430 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 82
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction autoPROC data scaling PHENIX phasing