3LQ3

Crystal structure of human choline kinase beta in complex with phosphorylated hemicholinium-3 and adenosine nucleotide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FEGdirect placement of protein coordinates of pdb entry 3FEG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52910.1M sodium cacodylate, 30% PEG4000, 0.2M ammonium sulfate. Protein buffer: 0.01M TRIS pH 8.0, 0.5M sodium chloride, 0.005M magnesium chloride, 0.01M dtt. Ligands: 0.003M hemicholinium-3, 0.005M atp., vapor diffusion, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1442.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.175α = 90
b = 73.206β = 117.97
c = 62.426γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC Q3152009-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97915APS19-ID

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
11.424099.90.0510.33.773581
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)
1.421.441000.9013.63673

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 DIFFRACTIONTHROUGHOUTdirect placement of protein coordinates of pdb entry 3FEG1.423073434370599.8760.1880.1870.213RANDOM13.708
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]
-0.05-0.0370.067-0.052
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.055
r_dihedral_angle_4_deg15.699
r_dihedral_angle_3_deg11.82
r_dihedral_angle_1_deg5.465
r_scangle_it3.476
r_scbond_it2.226
r_mcangle_it1.54
r_angle_refined_deg1.498
r_angle_other_deg0.876
r_mcbond_it0.875
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.055
r_dihedral_angle_4_deg15.699
r_dihedral_angle_3_deg11.82
r_dihedral_angle_1_deg5.465
r_scangle_it3.476
r_scbond_it2.226
r_mcangle_it1.54
r_angle_refined_deg1.498
r_angle_other_deg0.876
r_mcbond_it0.875
r_mcbond_other0.245
r_chiral_restr0.085
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2753
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms92

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling