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SARS-CoV-1 3CLPro in complex with N-(4-(1H-imidazol-4-yl)phenyl)-2-(1H-benzo[d][1,2,3]triazol-1-yl)-N-(thiophen-3-ylmethyl)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 63.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.406 α = 90 b = 81.915 β = 104.981 c = 53.308 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) 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 1.55 32.281 96.98 0.08478 0.99 7.38 6.9 64988
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 1.55 1.606 0.99
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 1.6 32.281 64985 3275 99.666 0.186 0.1845 0.1901 0.2078 0.2104 28.96
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] 0.001 -0.002 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.291 r_dihedral_angle_4_deg 17.029 r_dihedral_angle_3_deg 12.758 r_dihedral_angle_1_deg 7.36 r_lrange_it 6.735 r_lrange_other 6.437 r_scangle_it 5.383 r_scangle_other 5.382 r_scbond_it 4.071 r_scbond_other 4.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.291 r_dihedral_angle_4_deg 17.029 r_dihedral_angle_3_deg 12.758 r_dihedral_angle_1_deg 7.36 r_lrange_it 6.735 r_lrange_other 6.437 r_scangle_it 5.383 r_scangle_other 5.382 r_scbond_it 4.071 r_scbond_other 4.069 r_mcangle_it 2.876 r_mcangle_other 2.875 r_mcbond_it 2.178 r_mcbond_other 2.176 r_angle_refined_deg 1.812 r_angle_other_deg 1.516 r_nbd_refined 0.224 r_symmetry_nbd_refined 0.218 r_nbd_other 0.198 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.097 r_symmetry_xyhbond_nbd_refined 0.096 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing