1UOD

Crystal structure of the dihydroxyacetone kinase from E. coli in complex with dihydroxyacetone-phosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15pH 5.00
Crystal Properties
Matthews coefficientSolvent content
2.5852.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.498α = 90
b = 97.055β = 90
c = 86.123γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
11.92594.60.04531.73.7608092

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.924.1156190169494.60.1680.1670.206RANDOM17.32
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]
-0.521.61-1.09
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.15
r_scbond_it4.185
r_dihedral_angle_1_deg3.76
r_mcangle_it3.494
r_mcbond_it2.413
r_angle_refined_deg1.718
r_symmetry_vdw_refined0.496
r_symmetry_hbond_refined0.239
r_nbd_refined0.229
r_xyhbond_nbd_refined0.173
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.15
r_scbond_it4.185
r_dihedral_angle_1_deg3.76
r_mcangle_it3.494
r_mcbond_it2.413
r_angle_refined_deg1.718
r_symmetry_vdw_refined0.496
r_symmetry_hbond_refined0.239
r_nbd_refined0.229
r_xyhbond_nbd_refined0.173
r_chiral_restr0.15
r_bond_refined_d0.015
r_gen_planes_refined0.001
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5068
Nucleic Acid Atoms
Solvent Atoms477
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement