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Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-245
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 5.8, 15% PEG6000, 3% DMSO
Crystal Properties Matthews coefficient Solvent content 1.99 38.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.333 α = 90 b = 52.913 β = 103.74 c = 45.604 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 2021-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL24XU 1 SPring-8 BL24XU
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 1.46 56.02 99.1 0.178 8.68 8.5 46005
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 1.46 1.49 9.082
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 7JKV 1.46 56.02 43680 2322 99.04 0.20088 0.19935 0.22893 0.1998 RANDOM 26.529
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] 0.91 0.04 -0.09 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.979 r_dihedral_angle_4_deg 18.802 r_dihedral_angle_3_deg 13.689 r_dihedral_angle_1_deg 7.283 r_long_range_B_refined 5.924 r_long_range_B_other 5.923 r_scangle_other 4.459 r_mcangle_it 3.026 r_mcangle_other 3.025 r_scbond_it 2.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.979 r_dihedral_angle_4_deg 18.802 r_dihedral_angle_3_deg 13.689 r_dihedral_angle_1_deg 7.283 r_long_range_B_refined 5.924 r_long_range_B_other 5.923 r_scangle_other 4.459 r_mcangle_it 3.026 r_mcangle_other 3.025 r_scbond_it 2.893 r_scbond_other 2.892 r_mcbond_it 2.023 r_mcbond_other 2.023 r_angle_refined_deg 1.644 r_angle_other_deg 1.408 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 119 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement Coot model building PDB_EXTRACT data extraction MOLREP phasing xia2 data reduction DIALS data scaling