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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 2.49 50.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.804 α = 90 b = 100.804 β = 90 c = 185.037 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 2025-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 2.3 50.4 98.5 0.098 0.995 5.2 4 195162 58.9
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 2.3 2.38 99.3 1.93 0.18 0.6
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 2.3 30.471 48185 2419 98.166 0.217 0.214 0.2143 0.2725 0.2722 Random Selection 70.179
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] 1.241 0.621 1.241 -4.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.082 r_dihedral_angle_3_deg 16.931 r_dihedral_angle_6_deg 13.602 r_lrange_it 12.806 r_scangle_it 9.964 r_mcangle_it 8.147 r_dihedral_angle_1_deg 7.662 r_scbond_it 6.831 r_mcbond_it 5.607 r_angle_refined_deg 1.635
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.082 r_dihedral_angle_3_deg 16.931 r_dihedral_angle_6_deg 13.602 r_lrange_it 12.806 r_scangle_it 9.964 r_mcangle_it 8.147 r_dihedral_angle_1_deg 7.662 r_scbond_it 6.831 r_mcbond_it 5.607 r_angle_refined_deg 1.635 r_nbtor_refined 0.313 r_nbd_refined 0.24 r_symmetry_nbd_refined 0.201 r_xyhbond_nbd_refined 0.17 r_chiral_restr 0.123 r_symmetry_xyhbond_nbd_refined 0.105 r_metal_ion_refined 0.076 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7664 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 151
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing