5FUT

Human choline kinase a1 in complex with compound 4-(dimethylamino)-1-{4-[4-(4-{[4-(pyrrolidin- 1-yl)pyridinium-1-yl]methyl}phenyl)butyl]benzyl}pyridinium (compound BR25)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G15PDB ENTRY 3G15

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5HSCKALPHA1 AT 20 MG/ML WAS PREINCUBATED AT ROOM TEMPERATURE WITH 12 MM OF COMPOUND BR25 IN BUFFER 25 MM TRIS/HCL, 150 MM NACL PH 7.5 (DMSO IS AT 5% FINAL CONCENTRATION IN THE MIX). THE SITTING-DROP VAPOUR DIFFUSION METHOD WAS USED TO PRODUCE CRYSTALS BY MIXING 0.5 MICROL OF THE PROTEIN SOLUTION AND AN EQUAL VOLUME OF MOTHER LIQUOR (20% PEG 5000 MME AND 0.2 M KSCN). TETRAGONAL CRYSTALS (SPACE GROUP P43212) GREW WITHIN 2-4 DAYS AND THEN WERE SOAKED FOR ONE DAY WITH 20 MM COMPOUND BR25 SOLVED IN 100% DMSO. THE CRYSTALS USED IN THIS STUDY WERE CRYOPROTECTED IN MOTHER LIQUOR SOLUTIONS CONTAINING 20 % ETHYLENGLYCOL AND FROZEN IN A NITROGEN GAS STREAM COOLED TO 100 K.
Crystal Properties
Matthews coefficientSolvent content
2.3347.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.364α = 90
b = 61.364β = 90
c = 219.705γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOCALBAXALOC

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
11.62099.90.0444.225.45671944.222
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)
11.61.691000.676.626.2

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 3G151.619.7011.3456602160099.990.18150.18090.205
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_d17.271
f_angle_d1.065
f_chiral_restr0.051
f_bond_d0.007
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2944
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms74

Software

Software
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
MOLREPphasing