4FQF

Crystal structure of a thionitrate intermediate of human aldehyde dehydrogenase-2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O05 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.4293100 mM bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (Bis-TRIS), 25% PEG 3350, 60 mM urea; 13.3 mM magnesium chloride, 8.9 mM tris(2-carboxyethyl)phosphine (TCEP), 4.4 mM NAD+, 45.8 mM glucose, crystals have been soaked with glyceryl trinitrate (GTN), pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0540

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.862α = 90
b = 148.431β = 90
c = 176.005γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2010-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.81230EMBL/DESY, HAMBURGX13

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
12.28119.8399.10.0820.08214.56.452166681819
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.3999.90.2950.2955.76.4

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1o052.28119.8021.3480015402398.330.17190.16990.2092Random
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]
2.0467-0.1382-1.9086
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.077
f_angle_d0.889
f_chiral_restr0.058
f_bond_d0.012
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15138
Nucleic Acid Atoms
Solvent Atoms889
Heterogen Atoms220

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling