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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 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.383 α = 90 b = 102.383 β = 90 c = 189.068 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 2024-08-03 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 2.2 37.81 99 0.103 0.998 6.7 5.7 58396 62.4
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 2.2 2.32 100 3.38 0.17 0.5 5.8
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 2.2 30.668 58288 2921 98.854 0.224 0.222 0.2223 0.2715 0.2716 Random Selection 75.672
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] 1.123 0.562 1.123 -3.643
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.869 r_dihedral_angle_3_deg 14.762 r_dihedral_angle_6_deg 11.442 r_lrange_it 7.588 r_dihedral_angle_1_deg 6.878 r_scangle_it 4.75 r_mcangle_it 3.985 r_scbond_it 2.838 r_mcbond_it 2.456 r_angle_refined_deg 1.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.869 r_dihedral_angle_3_deg 14.762 r_dihedral_angle_6_deg 11.442 r_lrange_it 7.588 r_dihedral_angle_1_deg 6.878 r_scangle_it 4.75 r_mcangle_it 3.985 r_scbond_it 2.838 r_mcbond_it 2.456 r_angle_refined_deg 1.105 r_nbtor_refined 0.304 r_nbd_refined 0.208 r_symmetry_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.141 r_xyhbond_nbd_refined 0.124 r_metal_ion_refined 0.118 r_chiral_restr 0.094 r_gen_planes_refined 0.003 r_bond_refined_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7647 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing