2R5N

Crystal structure of transketolase from Escherichia coli in noncovalent complex with acceptor aldose ribose 5-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QGDPDB entry 1QGD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.928150 mM glycyl-glycine, 10 mM thiamin diphosphate, 5 mM calcium chloride, 19-22% PEG6000, 1% glycerol, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
2.0840.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.969α = 90
b = 101.738β = 90
c = 132.859γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2007-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.53594.70.1110.1114.912.11840351841803323.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5868.70.9880.9880.85.319193

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-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1QGD1.635160722159774802899.410.1690.1640.1630.196RANDOM12.34
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]
-0.410.060.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.578
r_dihedral_angle_4_deg16.461
r_dihedral_angle_3_deg11.503
r_dihedral_angle_1_deg5.623
r_scangle_it2.533
r_scbond_it1.634
r_angle_refined_deg1.23
r_mcangle_it0.867
r_mcbond_it0.506
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.578
r_dihedral_angle_4_deg16.461
r_dihedral_angle_3_deg11.503
r_dihedral_angle_1_deg5.623
r_scangle_it2.533
r_scbond_it1.634
r_angle_refined_deg1.23
r_mcangle_it0.867
r_mcbond_it0.506
r_nbtor_refined0.305
r_nbd_refined0.197
r_symmetry_vdw_refined0.167
r_metal_ion_refined0.135
r_xyhbond_nbd_refined0.109
r_symmetry_hbond_refined0.097
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10198
Nucleic Acid Atoms
Solvent Atoms1628
Heterogen Atoms160

Software

Software
Software NamePurpose
d*TREKdata scaling
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction