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Spirooxindole inhibitor CG-1062 complexed with SARS-Cov-2 3CL protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5R7Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2 M LiCl, 0.1 M Bis-Tris pH 6.5, 13%(w/v) polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 1.97 37.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.28 α = 90 b = 53.72 β = 100.517 c = 114.396 γ = 90
Symmetry Space Group I 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 100 CCD RIGAKU 2022-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54187
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.964 28.134 91.99 0.996 11.91 2.9 17882
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 1.964 2.034 0.897
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.964 28.134 17869 899 91.966 0.221 0.2186 0.2244 0.2597 0.2683 23.435
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] -0.141 0.225 0.872 -0.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.308 r_dihedral_angle_4_deg 18.495 r_dihedral_angle_3_deg 14.698 r_dihedral_angle_1_deg 8.086 r_lrange_it 4.733 r_lrange_other 4.719 r_scangle_it 3.132 r_scangle_other 3.132 r_mcangle_it 2.936 r_mcangle_other 2.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.308 r_dihedral_angle_4_deg 18.495 r_dihedral_angle_3_deg 14.698 r_dihedral_angle_1_deg 8.086 r_lrange_it 4.733 r_lrange_other 4.719 r_scangle_it 3.132 r_scangle_other 3.132 r_mcangle_it 2.936 r_mcangle_other 2.936 r_scbond_it 1.964 r_scbond_other 1.963 r_mcbond_it 1.839 r_mcbond_other 1.834 r_angle_refined_deg 1.523 r_angle_other_deg 1.305 r_nbd_refined 0.21 r_nbd_other 0.195 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.149 r_symmetry_nbd_refined 0.13 r_symmetry_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2323 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing