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SARS-CoV-1 3CLPro in complex with 2-(1H-benzo[d][1,2,3]triazol-1-yl)-N-(4-(pyridin-3-yl)phenyl)-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 63.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.685 α = 90 b = 82.471 β = 105.228 c = 53.297 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 1.85 40 99.42 0.019 5.77 7.4 38249
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 1.85 1.916 94.9 0.985
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 1.85 32.319 38249 1905 98.973 0.181 0.179 0.1861 0.2152 0.2196 34.883
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] -0.095 -0.293 0.042 0.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.968 r_dihedral_angle_4_deg 15.744 r_dihedral_angle_3_deg 15.501 r_lrange_it 8.085 r_lrange_other 8 r_dihedral_angle_1_deg 7.541 r_scangle_it 6.663 r_scangle_other 6.662 r_scbond_it 4.852 r_scbond_other 4.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.968 r_dihedral_angle_4_deg 15.744 r_dihedral_angle_3_deg 15.501 r_lrange_it 8.085 r_lrange_other 8 r_dihedral_angle_1_deg 7.541 r_scangle_it 6.663 r_scangle_other 6.662 r_scbond_it 4.852 r_scbond_other 4.85 r_mcangle_it 3.792 r_mcangle_other 3.792 r_mcbond_it 3.1 r_mcbond_other 3.099 r_angle_refined_deg 1.851 r_angle_other_deg 1.51 r_nbd_other 0.253 r_nbd_refined 0.216 r_symmetry_nbd_other 0.188 r_symmetry_nbd_refined 0.186 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.098 r_symmetry_xyhbond_nbd_refined 0.087 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.013 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 273 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing