4L1O

Crystal structure of human ALDH3A1 with inhibitor 1-{[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]methyl}-1H-indole-2,3-dione


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SZAPDB entry 3SZA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5298.150.2 M Potassium Acetate, 20% PEG 3350, (3 microlitres of 3mg/ml of ALDH3A1+ 3 microlitres of mother liquor), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.15K
Crystal Properties
Matthews coefficientSolvent content
2.1642.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.257α = 90
b = 86.396β = 90
c = 170.225γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++OSMIC CONFOCAL BLUE2011-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.35090.60.1460.0616.263.4373990.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3488.10.1466.72.72921

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3SZA2.347.9537399199095.980.179360.176860.22513RANDOM18.47
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]
-0.880.370.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.161
r_dihedral_angle_3_deg12.65
r_dihedral_angle_4_deg10.917
r_dihedral_angle_1_deg5.494
r_angle_refined_deg1.089
r_angle_other_deg0.724
r_chiral_restr0.056
r_bond_refined_d0.005
r_bond_other_d0.003
r_gen_planes_refined0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.161
r_dihedral_angle_3_deg12.65
r_dihedral_angle_4_deg10.917
r_dihedral_angle_1_deg5.494
r_angle_refined_deg1.089
r_angle_other_deg0.724
r_chiral_restr0.056
r_bond_refined_d0.005
r_bond_other_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7019
Nucleic Acid Atoms
Solvent Atoms648
Heterogen Atoms48

Software

Software
Software NamePurpose
HKL-3000data collection
AMoREphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling