3UNI

Crystal Structure of Bovine Milk Xanthine Dehydrogenase with NADH Bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FO4PDB Entry 1FO4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Sitting Drop Batch Slide7.529312 mg/ml Xanthine Dehydrogenase (from Bovine Milk), 8 % Polyethylene Glycol 4000, 30 % Glycerol, 5 mM Dithiothreitol, 0.5 mM Sodium Salicylate, 0.2 m Ethylenediaminetetraacetic Acid, 16.65 mM Sodium Pyrophosphate (pH 8.5), 25 mM Potasium Phosphate (pH 6.5). , Sitting Drop Batch Slide, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.5752.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.036α = 90
b = 146.698β = 106.03
c = 107.016γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 42000-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A1.0000Photon FactoryBL-6A

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
12.22099.90.0914.87.11150203149846-3-3
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)
12.22.2499.90.3773.643.77520

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry 1FO42.22014375814154722110.1980.24Random
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
c_angle_deg1.3
c_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20001
Nucleic Acid Atoms
Solvent Atoms1140
Heterogen Atoms350

Software

Software
Software NamePurpose
ADSCdata collection
EPMRphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling