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Crystal structure of SARS-CoV-2 3CL protease in complex with a methylcyclohexyl 2-pyrrolidone inhibitor (S-enantiomer)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XMK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 25% w/v PEG1500, 100 mM MMT, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.22 44.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.042 α = 90 b = 98.604 β = 107.62 c = 58.349 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 Bruker PHOTON III 2022-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5418
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 1.85 46.31 100 0.105 0.109 0.027 0.999 19 15.4 50633
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 1.85 1.89 100 1.645 1.739 0.561 0.764 9.5
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 1.85 46.31 1.08 50595 2512 99.9 0.1852 0.1829 0.1894 0.2291 0.2312
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 16.707 f_angle_d 1.076 f_chiral_restr 0.06 f_bond_d 0.011 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4520 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 139
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing