6K0I

Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP-Glc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EK6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277.1530% (v/v) PEG 400, 0.2 M MgCl, 0.1 M HEPES-NaOH (pH 7.5), 10 mM UDP-Glc
Crystal Properties
Matthews coefficientSolvent content
3.0960.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.359α = 90
b = 70.359β = 90
c = 322.553γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2014-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.000Photon FactoryAR-NW12A

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
11.85098.10.09537.81844500
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)
11.81.83970.4557.718.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1EK61.836.7842233224898.320.16250.1610.1898RANDOM17.93
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.111
r_dihedral_angle_4_deg15.967
r_dihedral_angle_3_deg12.537
r_dihedral_angle_1_deg6.791
r_angle_refined_deg1.769
r_angle_other_deg1.098
r_chiral_restr0.094
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.111
r_dihedral_angle_4_deg15.967
r_dihedral_angle_3_deg12.537
r_dihedral_angle_1_deg6.791
r_angle_refined_deg1.769
r_angle_other_deg1.098
r_chiral_restr0.094
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2588
Nucleic Acid Atoms
Solvent Atoms322
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing