3SZB

Crystal structure of human ALDH3A1 modified with the beta-elimination product of Aldi-1; 1-phenyl- 2-propen-1-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AD3PDB entry 1AD3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2980.2 M potassium acetate, 18% PEG 3350, vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1342.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.377α = 90
b = 85.727β = 90
c = 169.555γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9869APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.515097.70.05813.54.41374980.226.6
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)
11.511.5497.80.393.46822

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 1AD31.5150137383687897.550.17990.17880.2021RANDOM20.6178
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]
-1.241.240.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.632
r_dihedral_angle_4_deg14.123
r_dihedral_angle_3_deg12.53
r_dihedral_angle_1_deg6.135
r_scangle_it3.869
r_scbond_it2.396
r_angle_refined_deg1.508
r_mcangle_it1.423
r_mcbond_it0.842
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.632
r_dihedral_angle_4_deg14.123
r_dihedral_angle_3_deg12.53
r_dihedral_angle_1_deg6.135
r_scangle_it3.869
r_scbond_it2.396
r_angle_refined_deg1.508
r_mcangle_it1.423
r_mcbond_it0.842
r_chiral_restr0.101
r_bond_refined_d0.015
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7019
Nucleic Acid Atoms
Solvent Atoms1158
Heterogen Atoms32

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
AMoREphasing