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SARS-CoV-1 3CLPro in complex with 2-(1H-benzo[d][1,2,3]triazol-1-yl)-N-(3-chlorobenzyl)-N-(4-(2-oxo-1,2-dihydropyridin-3-yl)phenyl)acetamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VB3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 295 10% PEG 6000, 0.1M MES, 1mM DTT, 1mM EDTA, 3% DMSO, 10% Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.37 63.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.539 α = 90 b = 82.712 β = 105.299 c = 53.2 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 80 CCD RAYONIX MX-300 2020-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.978 APS 21-ID-F
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 1.686 32.356 99.5 0.029 17.06 7.4 50084
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 1.686 1.75 0.2421
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 3VB3 1.686 32.356 50084 2506 98.847 0.148 0.1456 0.1566 0.1917 0.1967 38.825
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] -0.169 -0.239 0.531 -0.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.351 r_dihedral_angle_4_deg 16.714 r_dihedral_angle_3_deg 14.495 r_scangle_it 8.04 r_scangle_other 8.038 r_scbond_it 7.63 r_scbond_other 7.627 r_dihedral_angle_1_deg 7.368 r_lrange_it 7.288 r_lrange_other 7.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.351 r_dihedral_angle_4_deg 16.714 r_dihedral_angle_3_deg 14.495 r_scangle_it 8.04 r_scangle_other 8.038 r_scbond_it 7.63 r_scbond_other 7.627 r_dihedral_angle_1_deg 7.368 r_lrange_it 7.288 r_lrange_other 7.143 r_rigid_bond_restr 5.374 r_mcangle_it 4.884 r_mcangle_other 4.883 r_mcbond_it 4.444 r_mcbond_other 4.444 r_angle_refined_deg 1.927 r_angle_other_deg 1.523 r_nbd_other 0.232 r_nbd_refined 0.221 r_symmetry_nbd_refined 0.199 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.137 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing