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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 2.46 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.336 α = 90 b = 100.336 β = 90 c = 185.077 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 2.9 50.3 98.9 0.184 0.987 3.7 4 24254 67.4
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 2.9 3.08 99.7 1.42 0.29 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 2.9 30.471 24153 1125 98.215 0.232 0.2294 0.2301 0.2964 0.2963 Random Selection 84.489
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] 2.699 1.35 2.699 -8.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.614 r_dihedral_angle_3_deg 14.656 r_dihedral_angle_6_deg 10.799 r_lrange_it 8.018 r_dihedral_angle_1_deg 6.809 r_scangle_it 3.948 r_mcangle_it 3.565 r_scbond_it 2.235 r_mcbond_it 2.082 r_angle_refined_deg 1.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.614 r_dihedral_angle_3_deg 14.656 r_dihedral_angle_6_deg 10.799 r_lrange_it 8.018 r_dihedral_angle_1_deg 6.809 r_scangle_it 3.948 r_mcangle_it 3.565 r_scbond_it 2.235 r_mcbond_it 2.082 r_angle_refined_deg 1.031 r_nbtor_refined 0.301 r_nbd_refined 0.212 r_symmetry_nbd_refined 0.145 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.083 r_symmetry_xyhbond_nbd_refined 0.058 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_metal_ion_refined 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7645 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing