4A0R

Structure of bifunctional DAPA aminotransferase-DTB synthetase from Arabidopsis thaliana bound to dethiobiotin (DTB).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherNATIVE DETHIOBIOTIN SYNTHETASE- DIAMINOPELARGONIC ACID AMINOTRANSFERASE FROM ARABIDOPSIS THALIANA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2 M AMMONIUM TARTRATE PH 6.2, 15 % PEG 3350.
Crystal Properties
Matthews coefficientSolvent content
1.9135.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 246.67α = 90
b = 76.63β = 108.02
c = 79.84γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.6840.4499.70.159.954.240026-334.68
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)
12.682.7599.80.761.834.2

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTNATIVE DETHIOBIOTIN SYNTHETASE- DIAMINOPELARGONIC ACID AMINOTRANSFERASE FROM ARABIDOPSIS THALIANA2.6840.43640012200699.820.18810.18440.25934.9
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]
-2.9779-3.0183.5817-0.6038
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.232
f_angle_d1.253
f_chiral_restr0.077
f_bond_d0.009
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11470
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms80

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing