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Spirooxindole inhibitor CG-1059 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, HANGING DROP 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 1.96 37.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.09 α = 90 b = 53.93 β = 100.776 c = 114.135 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 2022-08-18 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 1.97 27.516 91.66 0.996 12.68 3.2 17881
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 1.97 2.04 0.942
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 1.97 27.516 17587 908 91.661 0.231 0.2285 0.2338 0.2743 0.276 26.974
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] -0.546 0.604 0.971 -0.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.98 r_dihedral_angle_4_deg 16.278 r_dihedral_angle_3_deg 14.95 r_dihedral_angle_1_deg 7.886 r_lrange_it 5.306 r_lrange_other 5.27 r_scangle_it 3.546 r_scangle_other 3.545 r_mcangle_it 3.383 r_mcangle_other 3.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.98 r_dihedral_angle_4_deg 16.278 r_dihedral_angle_3_deg 14.95 r_dihedral_angle_1_deg 7.886 r_lrange_it 5.306 r_lrange_other 5.27 r_scangle_it 3.546 r_scangle_other 3.545 r_mcangle_it 3.383 r_mcangle_other 3.382 r_scbond_it 2.232 r_scbond_other 2.232 r_mcbond_other 2.129 r_mcbond_it 2.128 r_angle_refined_deg 1.523 r_angle_other_deg 1.302 r_nbd_refined 0.206 r_symmetry_xyhbond_nbd_refined 0.186 r_symmetry_nbd_other 0.183 r_nbd_other 0.171 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.147 r_symmetry_nbd_refined 0.134 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.067 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 2347 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing