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Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-276-5Br
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8UH5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M HEPES pH 7.5, 16% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.04 39.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.339 α = 68.31 b = 52.972 β = 87.69 c = 61.907 γ = 89.98
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 4M 2023-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.979497 NSLS-II 19-ID
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 1.79 50 90.5 0.995 15.73 1.6 49937
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 1.8 1.83 64.9 0.896 2.38 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.79 33.61 42245 2130 87.53 0.19235 0.19054 0.1997 0.22746 0.2311 RANDOM 21.823
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] -0.02 0.02 0.12 -0.23 0.08 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.59 r_dihedral_angle_3_deg 14.093 r_dihedral_angle_1_deg 7.323 r_long_range_B_refined 5.407 r_long_range_B_other 5.406 r_scangle_other 4.124 r_mcangle_it 2.699 r_mcangle_other 2.698 r_scbond_it 2.651 r_scbond_other 2.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.59 r_dihedral_angle_3_deg 14.093 r_dihedral_angle_1_deg 7.323 r_long_range_B_refined 5.407 r_long_range_B_other 5.406 r_scangle_other 4.124 r_mcangle_it 2.699 r_mcangle_other 2.698 r_scbond_it 2.651 r_scbond_other 2.651 r_angle_refined_deg 1.81 r_mcbond_it 1.794 r_mcbond_other 1.794 r_angle_other_deg 0.63 r_chiral_restr 0.102 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 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 4734 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling MOLREP phasing