5XU2

Crystal Structure of Transketolase in complex with TPP_III and fructose-6-phosphate from Pichia Stipitis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HYV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1M MES, 0.1M NaCl, PEG 400
Crystal Properties
Matthews coefficientSolvent content
3.0960.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.269α = 90
b = 185.284β = 90
c = 98.932γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2015-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11NSRRCBL15A1

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
10.9730990.119.910.7542392
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)
10.9710.66

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 REPLACEMENTTHROUGHOUT5HYV0.97305147612749799.660.137080.136610.14568RANDOM10.945
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]
-0.190.41-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.592
r_sphericity_free26.213
r_dihedral_angle_4_deg16.024
r_rigid_bond_restr11.801
r_dihedral_angle_3_deg11.764
r_sphericity_bonded6.202
r_dihedral_angle_1_deg5.976
r_long_range_B_refined2.843
r_long_range_B_other2.843
r_angle_other_deg1.976
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.592
r_sphericity_free26.213
r_dihedral_angle_4_deg16.024
r_rigid_bond_restr11.801
r_dihedral_angle_3_deg11.764
r_sphericity_bonded6.202
r_dihedral_angle_1_deg5.976
r_long_range_B_refined2.843
r_long_range_B_other2.843
r_angle_other_deg1.976
r_scangle_other1.897
r_angle_refined_deg1.68
r_scbond_it1.577
r_scbond_other1.577
r_mcangle_it1.016
r_mcangle_other1.016
r_mcbond_it0.785
r_mcbond_other0.784
r_chiral_restr0.112
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.006
r_bond_other_d0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5133
Nucleic Acid Atoms
Solvent Atoms785
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling