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Crystal structure of SARS main protease in complex with GC376
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YGQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M Hepes pH7.5, 10% PEG8000, 8% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.19 61.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.123 α = 92.045 b = 61.575 β = 102.831 c = 67.902 γ = 109.296
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 2022-09-29 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 2.17 57.17 93.2 0.044 14.5 3.1 40341 42.3523509821
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 2.17 2.29 0.404
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 2.17 35.9280447003 1.96834197979 40305 1964 93.0981913935 0.214009498664 0.212486621199 0.2139 0.243449837413 0.2446 52.0704091299
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 4.57073355729 f_angle_d 1.01966962563 f_chiral_restr 0.053074341244 f_bond_d 0.00846648819982 f_plane_restr 0.00626510376626
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4339 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing