4YH5

Lipomyces starkeyi levoglucosan kinase bound to ADP and Manganese


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2293Equal volumes of reservoir buffer (18% PEG 4000, 0.1 M sodium acetate, 0.1 M Tris pH 7.2) and LGK (7 mg/ml) in crystallization buffer (50 mM NaCl, 2 mM ADP, 5 mM Manganese(II) chloride tetrahydrate, 25 mM levoglucosan, 0.5 mM TCEP, 20 mM Tris pH 7.5) were mixed.
Crystal Properties
Matthews coefficientSolvent content
3.9769.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.44α = 90
b = 114.44β = 90
c = 232.484γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002012-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-11.89199CLSI08ID-1

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
11.947.2199.90.1044.219.7121746
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)
11.920.569

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.947.211.08121618608199.80.1560.1550.174Random selection
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.251
f_angle_d1.069
f_chiral_restr0.07
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6654
Nucleic Acid Atoms
Solvent Atoms1032
Heterogen Atoms66

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHENIXphasing