3G15

Crystal structure of human choline kinase alpha in complex with hemicholinium-3 and ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I7QPDB ENTRY 2I7Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.529125% PEG-3350, 0.2M lithium sulfate, 0.1M HEPES. Crystallization sample buffer: 0.01M TRIS pH 8.0, 0.5M sodium chloride, 0.005M magnesium chloride, 0.01M DTT, 0.003M hemicholinium-3, 0.005M ADP., vapor diffusion, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3247.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.802α = 90
b = 118.986β = 90
c = 131.039γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2008-02-14SINGLE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.96863APS23-ID-B

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
11.750970.06911.46.593657
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)
1.71.7675.60.7972.67162

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2I7Q1.73093409212296.6940.2210.220.257thin shells (sftools)22.163
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]
-0.5221.292-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.119
r_dihedral_angle_4_deg13.077
r_dihedral_angle_3_deg12.758
r_dihedral_angle_1_deg5.454
r_scangle_it3.479
r_mcangle_it2.992
r_scbond_it2.41
r_angle_other_deg2.189
r_mcbond_it2.012
r_angle_refined_deg1.388
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.119
r_dihedral_angle_4_deg13.077
r_dihedral_angle_3_deg12.758
r_dihedral_angle_1_deg5.454
r_scangle_it3.479
r_mcangle_it2.992
r_scbond_it2.41
r_angle_other_deg2.189
r_mcbond_it2.012
r_angle_refined_deg1.388
r_mcbond_other0.586
r_chiral_restr0.083
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5354
Nucleic Acid Atoms
Solvent Atoms324
Heterogen Atoms149

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building
MolProbitymodel building
ARP/wARPmodel building