3UPT

Crystal structure of a transketolase from Burkholderia pseudomallei bound to TPP, calcium and ribose-5-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UK1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289ButhA.01294.a.A1 at 38 mg/mL with 5 mM TPP, 5 mM ribose-5-phosphate, 5 mM CaCl2 against PACT screen condition G2, 0.2 M NaBr, 0.1 M BisTris propane pH 7.5, 20% PEG 3350 cryo-protected with crystallant, compounds and 25% ethylene glycol; crystal tracking ID 227593g2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.5151.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.98α = 90
b = 146.98β = 90
c = 142.87γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97740ALS5.0.1

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
12.45099.70.15217.5261439-326.634
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)
12.42.461000.5584.92

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 REPLACEMENTTHROUGHOUT3UK12.45061438311599.740.15340.15090.2001RANDOM19.5631
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]
-0.64-0.641.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.372
r_dihedral_angle_4_deg18.162
r_dihedral_angle_3_deg13.518
r_dihedral_angle_1_deg6.234
r_angle_refined_deg1.464
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10046
Nucleic Acid Atoms
Solvent Atoms821
Heterogen Atoms86

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction