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SARS-CoV-1 3CLPro in complex with N-(4-(1H-pyrazol-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 3.4 63.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.508 α = 90 b = 82.109 β = 104.657 c = 53.384 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 1.707 32.359 99.75 0.054 2.59 6.4 48877
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 1.707 1.77 0.3218
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 1.707 32.34 48877 2450 99.291 0.17 0.1674 0.1768 0.2156 0.2211 33.653
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] -0.345 0.357 0.949 -0.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.735 r_dihedral_angle_4_deg 19.963 r_dihedral_angle_3_deg 15.086 r_dihedral_angle_1_deg 7.752 r_scangle_it 6.673 r_scangle_other 6.671 r_lrange_it 6.249 r_lrange_other 6.224 r_scbond_it 6.155 r_scbond_other 6.153
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.735 r_dihedral_angle_4_deg 19.963 r_dihedral_angle_3_deg 15.086 r_dihedral_angle_1_deg 7.752 r_scangle_it 6.673 r_scangle_other 6.671 r_lrange_it 6.249 r_lrange_other 6.224 r_scbond_it 6.155 r_scbond_other 6.153 r_rigid_bond_restr 4.832 r_mcangle_other 4.492 r_mcangle_it 4.47 r_mcbond_it 4.015 r_mcbond_other 3.949 r_angle_refined_deg 1.959 r_angle_other_deg 1.502 r_nbd_other 0.248 r_nbd_refined 0.22 r_symmetry_nbd_refined 0.203 r_symmetry_nbd_other 0.189 r_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.106 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.084 r_symmetry_xyhbond_nbd_other 0.079 r_bond_refined_d 0.016 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 2370 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing