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Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-277-5Cl
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 2.28 46.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.531 α = 90 b = 64.238 β = 90 c = 105.383 γ = 90
Symmetry Space Group P 21 21 2
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) 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 1.8 50 94.1 0.092 15.88 4.6 29303
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 1.8 1.83 66.5 0.393
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 1.8 32.14 25644 1362 91.99 0.16615 0.16442 0.177 0.19999 0.2097 RANDOM 22.448
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] -0.18 0.28 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.482 r_dihedral_angle_3_deg 12.238 r_dihedral_angle_1_deg 7.01 r_long_range_B_refined 6.441 r_long_range_B_other 6.44 r_scangle_other 4.731 r_mcangle_it 3.105 r_mcangle_other 3.104 r_scbond_it 3.075 r_scbond_other 3.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.482 r_dihedral_angle_3_deg 12.238 r_dihedral_angle_1_deg 7.01 r_long_range_B_refined 6.441 r_long_range_B_other 6.44 r_scangle_other 4.731 r_mcangle_it 3.105 r_mcangle_other 3.104 r_scbond_it 3.075 r_scbond_other 3.074 r_mcbond_it 2.017 r_mcbond_other 2.017 r_angle_refined_deg 1.819 r_angle_other_deg 0.604 r_chiral_restr 0.086 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 2367 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling MOLREP phasing