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Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-198
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JKV PDB entry 7JKV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.1 M MES pH 6.0, 15% polyethyene glycol (PEG) 6000 and 3% DMSO
Crystal Properties Matthews coefficient Solvent content 2.19 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.046 α = 90 b = 98.942 β = 106.28 c = 57.724 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 EIGER X 16M 2021-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.59 98.94 91.04 0.2221 5.59 8.3 76634
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.591 1.648 0.762
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 7JKV 1.59 55.47 72879 3732 98.27 0.19955 0.19725 0.2058 0.24566 0.2537 RANDOM 30.965
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] -1.14 -1.38 0.44 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.624 r_dihedral_angle_2_deg 12.039 r_dihedral_angle_1_deg 7.809 r_long_range_B_refined 7.226 r_long_range_B_other 7.225 r_scangle_other 4.936 r_mcangle_it 3.936 r_mcangle_other 3.935 r_scbond_it 3.418 r_scbond_other 3.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.624 r_dihedral_angle_2_deg 12.039 r_dihedral_angle_1_deg 7.809 r_long_range_B_refined 7.226 r_long_range_B_other 7.225 r_scangle_other 4.936 r_mcangle_it 3.936 r_mcangle_other 3.935 r_scbond_it 3.418 r_scbond_other 3.417 r_mcbond_it 2.584 r_mcbond_other 2.583 r_angle_refined_deg 1.561 r_angle_other_deg 0.573 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4666 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement DIALS data reduction MOLREP phasing Coot model building xia2 data scaling