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Structure-activity-relationship studies of guanidine-based ALDH1B1 inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 PEG 4000, Glycerol, ethyleneglycol, bicine/tris
Crystal Properties Matthews coefficient Solvent content 2.51 50.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.196 α = 90 b = 101.196 β = 90 c = 184.942 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS EIGER2 XE 16M Kirkpatrick-Baez (KB) optical mirrors 2022-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.97946 SSRL BL12-1
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 2.1 48.8 100 0.148 0.99 8 8.7 64715 34.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 100 1.097 0.773 2.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 30.64 64588 3315 99.822 0.183 0.1803 0.1807 0.2369 0.2372 Random Selection 43.577
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] 0.898 0.449 0.898 -2.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.026 r_dihedral_angle_3_deg 15.838 r_dihedral_angle_6_deg 14.4 r_lrange_it 8.689 r_scangle_it 7.579 r_dihedral_angle_1_deg 7.206 r_scbond_it 5.269 r_mcangle_it 4.826 r_mcbond_it 3.633 r_angle_refined_deg 1.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.026 r_dihedral_angle_3_deg 15.838 r_dihedral_angle_6_deg 14.4 r_lrange_it 8.689 r_scangle_it 7.579 r_dihedral_angle_1_deg 7.206 r_scbond_it 5.269 r_mcangle_it 4.826 r_mcbond_it 3.633 r_angle_refined_deg 1.782 r_metal_ion_refined 0.321 r_nbtor_refined 0.312 r_nbd_refined 0.218 r_symmetry_nbd_refined 0.195 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.137 r_symmetry_xyhbond_nbd_refined 0.116 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7704 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 169
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing