7WRT

X-ray structure ofThermus thermophilus HB8 transketorase demonstrate in complex with TPP and D-erythrose-4-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E6K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP298100mM imidazole/MES buffer pH 6.5, 20%(v/v) ethylene glycol, 10% (w/v) PEG 8000, 24mM of D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, and N-acetyl-D-glucosamine
Crystal Properties
Matthews coefficientSolvent content
2.3347.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.68α = 72.308
b = 88.86β = 88.696
c = 117.37γ = 73.459
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.2541.8698.10.99818.63.5124659
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.310.839

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2E6K2.2541.86124659625198.1520.2050.2020.25455.66
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]
-0.409-0.1110.0050.057-0.0840.172
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.727
r_dihedral_angle_4_deg17.546
r_dihedral_angle_3_deg17.407
r_lrange_it9.752
r_lrange_other9.752
r_dihedral_angle_1_deg7.712
r_mcangle_it7.239
r_mcangle_other7.239
r_scangle_it7.237
r_scangle_other7.237
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.727
r_dihedral_angle_4_deg17.546
r_dihedral_angle_3_deg17.407
r_lrange_it9.752
r_lrange_other9.752
r_dihedral_angle_1_deg7.712
r_mcangle_it7.239
r_mcangle_other7.239
r_scangle_it7.237
r_scangle_other7.237
r_mcbond_it5.185
r_mcbond_other5.185
r_scbond_it5.013
r_scbond_other5.013
r_angle_refined_deg1.642
r_angle_other_deg1.256
r_nbd_refined0.212
r_symmetry_nbd_other0.187
r_symmetry_xyhbond_nbd_refined0.183
r_metal_ion_refined0.174
r_xyhbond_nbd_refined0.167
r_nbtor_refined0.166
r_nbd_other0.161
r_symmetry_nbd_refined0.111
r_symmetry_xyhbond_nbd_other0.104
r_symmetry_nbtor_other0.079
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_xyhbond_nbd_other0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20280
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms156

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing