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Crystal structure of SARS-CoV-2 main protease in complex with inhibitor TKB-248
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, SITTING DROP 298 0.1 M MES, pH 5.8, 15% PEG6000, 3% DMSO
Crystal Properties Matthews coefficient Solvent content 2.08 40.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.403 α = 90 b = 53.926 β = 101.63 c = 45.678 γ = 90
Symmetry Space Group C 1 2 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 2021-10-09 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) 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 2 56.52 99.9 0.997 9.16 8.6 18600
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 2 2.04 0.672
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 2 56.52 17665 934 99.86 0.19252 0.1897 0.2013 0.24722 0.2194 RANDOM 42.805
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] 1.87 -0.53 -0.01 -1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.957 r_long_range_B_refined 8.234 r_long_range_B_other 8.233 r_dihedral_angle_1_deg 8.109 r_dihedral_angle_2_deg 7.639 r_scangle_other 6.286 r_mcangle_it 4.973 r_mcangle_other 4.972 r_scbond_it 4.384 r_scbond_other 4.383
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.957 r_long_range_B_refined 8.234 r_long_range_B_other 8.233 r_dihedral_angle_1_deg 8.109 r_dihedral_angle_2_deg 7.639 r_scangle_other 6.286 r_mcangle_it 4.973 r_mcangle_other 4.972 r_scbond_it 4.384 r_scbond_other 4.383 r_mcbond_it 3.609 r_mcbond_other 3.608 r_angle_refined_deg 1.648 r_angle_other_deg 0.624 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 2337 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Coot model building MOLREP phasing xia2 data reduction DIALS data scaling