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Crystal structure of human ALDH1A1 bound to compound (R)-28
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DUM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 293 100 mM sodium BisTris, pH 6.4, 9% PEG3350, 200 mM NaCl, and 5-10 mM YbCl3, 250 uM 1-methyl-5-phenyl-6-((1-(pyridin-2-yl)ethyl)thio)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one and 1% v/v DMSO
Crystal Properties Matthews coefficient Solvent content 2.24 45.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.032 α = 90 b = 109.032 β = 90 c = 82.888 γ = 90
Symmetry Space Group P 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210r 2018-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.98 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 109.03 98.4 0.106 0.112 0.036 7.7 9.5 39319
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 97.5 0.776 0.821 0.267 0.952 9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6DUM 1.9 109.03 36888 1974 97.23 0.2074 0.2045 0.2625 0.2668 RANDOM 40.803
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] -2.31 -2.31 4.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.993 r_dihedral_angle_4_deg 15.101 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_1_deg 6.291 r_angle_refined_deg 1.368 r_angle_other_deg 0.901 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.993 r_dihedral_angle_4_deg 15.101 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_1_deg 6.291 r_angle_refined_deg 1.368 r_angle_other_deg 0.901 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3814 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 74
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing