1UN8 | pdb_00001un8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.519.924605339761000.20.1960.240.246RANDOM29.42
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7976
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement