5XPS

Crystal Structure of Transketolase in complex with erythrose-4-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, PEG400
Crystal Properties
Matthews coefficientSolvent content
3.1861.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.149α = 90
b = 185.246β = 90
c = 98.71γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-10-11MSINGLE 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)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
11.0792.6299.90.0580.0720.77.9403372
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.070.73

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 REPLACEMENTTHROUGHOUT5HYV1.0792.623681161909195.730.119190.118540.13154RANDOM19.413
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]
-0.22-0.410.63
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.028
r_dihedral_angle_2_deg34.781
r_dihedral_angle_4_deg16.863
r_sphericity_bonded11.958
r_dihedral_angle_3_deg11.562
r_dihedral_angle_1_deg6.046
r_long_range_B_refined4.308
r_long_range_B_other4.308
r_rigid_bond_restr4.078
r_scangle_other3.359
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free35.028
r_dihedral_angle_2_deg34.781
r_dihedral_angle_4_deg16.863
r_sphericity_bonded11.958
r_dihedral_angle_3_deg11.562
r_dihedral_angle_1_deg6.046
r_long_range_B_refined4.308
r_long_range_B_other4.308
r_rigid_bond_restr4.078
r_scangle_other3.359
r_mcangle_it3.263
r_mcangle_other3.263
r_mcbond_it3.04
r_mcbond_other3.04
r_scbond_it2.872
r_scbond_other2.872
r_angle_refined_deg1.515
r_angle_other_deg1.286
r_chiral_restr0.095
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.002
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 Atoms5130
Nucleic Acid Atoms
Solvent Atoms948
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling