5J49

Crystal structure of UDP-glucose pyrophosporylase / UTP-glucose-1-phosphate uridylyltransferase from Burkholderia xenovorans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3JUJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5290Microlytic MCSG1 screen H7: 2M Ammonium sulphate, 100mM BisTris pH 5.5; BuxeA.00118.c.B1.PS02592 at 16mg/ml; cryo: 25% EG in two steps; tray 269868 h7, puck RPA3-4
Crystal Properties
Matthews coefficientSolvent content
2.4650

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.11α = 90
b = 134.11β = 90
c = 73.15γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252016-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.8501000.051133.2612.262217-322.63
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)
11.81.851000.535.27

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-VALUE3juj1.8501.3462144195399.970.17170.17060.207133.3583
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_d14.302
f_angle_d0.862
f_chiral_restr0.056
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4437
Nucleic Acid Atoms
Solvent Atoms433
Heterogen Atoms29

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
ARPmodel building
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction