2R8O

Transketolase from E. coli in complex with substrate D-xylulose-5-phosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.9281PEG 6000, glycerol, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
2.0941.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.138α = 90
b = 101.951β = 90
c = 133.258γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2006-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.8423EMBL/DESY, HAMBURGBW7B

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
11.4727.499.80.06711.611.320854220791429.7
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)
1.471.4999.20.31710.66843

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.4727.142208119207809209499.850.150.150.150.164RANDOM9.044
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]
0.01-0.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.166
r_dihedral_angle_4_deg17.318
r_dihedral_angle_3_deg11.153
r_dihedral_angle_1_deg5.622
r_scangle_it2.376
r_scbond_it1.553
r_angle_refined_deg1.28
r_mcangle_it0.825
r_mcbond_it0.534
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.166
r_dihedral_angle_4_deg17.318
r_dihedral_angle_3_deg11.153
r_dihedral_angle_1_deg5.622
r_scangle_it2.376
r_scbond_it1.553
r_angle_refined_deg1.28
r_mcangle_it0.825
r_mcbond_it0.534
r_nbtor_refined0.304
r_nbd_refined0.19
r_symmetry_vdw_refined0.176
r_metal_ion_refined0.139
r_symmetry_hbond_refined0.122
r_xyhbond_nbd_refined0.103
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10254
Nucleic Acid Atoms
Solvent Atoms1202
Heterogen Atoms126

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection