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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 2.52 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.922 α = 90 b = 100.922 β = 90 c = 187.431 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 BL12-1 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 2.4 35.81 99.2 0.109 0.999 6.7 5.7 43380 91.1
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 2.4 2.53 99.6 7.225 0.086 0.2 5.2
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 2.4 30.403 43292 2229 98.505 0.258 0.2555 0.2558 0.3063 0.3064 Random Selection 107.957
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] 2.137 1.069 2.137 -6.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.745 r_dihedral_angle_3_deg 15.203 r_lrange_it 10.072 r_dihedral_angle_6_deg 10.039 r_dihedral_angle_1_deg 6.744 r_scangle_it 5.463 r_mcangle_it 5.231 r_scbond_it 3.166 r_mcbond_it 3.133 r_angle_refined_deg 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.745 r_dihedral_angle_3_deg 15.203 r_lrange_it 10.072 r_dihedral_angle_6_deg 10.039 r_dihedral_angle_1_deg 6.744 r_scangle_it 5.463 r_mcangle_it 5.231 r_scbond_it 3.166 r_mcbond_it 3.133 r_angle_refined_deg 1.03 r_nbtor_refined 0.299 r_metal_ion_refined 0.23 r_nbd_refined 0.203 r_symmetry_nbd_refined 0.158 r_xyhbond_nbd_refined 0.138 r_symmetry_xyhbond_nbd_refined 0.1 r_chiral_restr 0.083 r_bond_refined_d 0.002 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7642 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing