6EDH

Taurine:2OG dioxygenase (TauD) bound to the vanadyl ion, taurine, and succinate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GY91GY9A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2980.1 M Na acetate, pH 4.25, and 24% (w/v) PEG 300
Crystal Properties
Matthews coefficientSolvent content
2.1542.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.41α = 90
b = 54.199β = 90
c = 87.385γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2017-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.7336.53990.0670.01923.2713.15893927.4529191957
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.7999.250.3251.9613.3

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 REPLACEMENTFREE R-VALUE1GY9A1.7300040165736.35364053691.336482226958911171298.96683802040.1834027611870.1827888088110.20476762038632.4592989629
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_d18.77926473
f_angle_d0.739142057799
f_chiral_restr0.0512155479686
f_bond_d0.00505745210407
f_plane_restr0.00445052146303
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4541
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms6

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
BALBESphasing
Cootmodel building