4X0T

Structure ALDH7A1 inactivated by 4-diethylaminobenzaldehyde and complexed with NAD+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J6L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293The reservoir contained 0.1 M magnesium formate dihydrate, 15% w/v PEG 3350 and 0.1 M Hepes. The enzyme stock solution included 3 mg/mL ALDH7A1, 200 micromolar 4-diethyaminobenzaldehyde and 5 mM NAD+.
Crystal Properties
Matthews coefficientSolvent content
2.3146.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.263α = 90
b = 160.263β = 90
c = 320.482γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSCUSTOM-MADETaurus-1 detector2014-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.000ALS4.2.2

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
12.459.5299.70.154127.58106730.27
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)
12.42.4595.41.0631.97.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2J6L2.459.521.3681030406899.60.1830.180.23538
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.925
f_angle_d0.682
f_chiral_restr0.025
f_bond_d0.003
f_plane_restr0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15133
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms228

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata scaling
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction