1UN8

Crystal structure of the dihydroxyacetone kinase of C. freundii (native form)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5pH 7.50
Crystal Properties
Matthews coefficientSolvent content
3.261.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.44α = 90
b = 124.59β = 90
c = 237.12γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM1AESRFBM1A

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
12.52596.80.06614.43.8501872

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 DIFFRACTIONMADTHROUGHOUT2.519.924605339761000.20.1960.246RANDOM29.42
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]
-2.47.13-4.73
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.447
r_scbond_it3.131
r_mcangle_it2.972
r_dihedral_angle_1_deg2.552
r_mcbond_it1.794
r_angle_refined_deg1.434
r_nbd_refined0.262
r_symmetry_vdw_refined0.247
r_symmetry_hbond_refined0.188
r_xyhbond_nbd_refined0.164
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.447
r_scbond_it3.131
r_mcangle_it2.972
r_dihedral_angle_1_deg2.552
r_mcbond_it1.794
r_angle_refined_deg1.434
r_nbd_refined0.262
r_symmetry_vdw_refined0.247
r_symmetry_hbond_refined0.188
r_xyhbond_nbd_refined0.164
r_chiral_restr0.12
r_bond_refined_d0.011
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 Atoms7976
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement