5FUT | pdb_00005fut

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)
Type	Source	Accession Code	Details
experimental model	PDB	3G15	PDB ENTRY 3G15

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5		HSCKALPHA1 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 coefficient	Solvent content
2.33	47.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.364	α = 90
b = 61.364	β = 90
c = 219.705	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC		ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.6	20	99.9	0.04	44.2	25.4		56719		44.2	22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.69	100		0.67	6.6	26.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3G15	1.6	19.701	1.34	56602	1600	99.99	0.1815	0.1809	0.18	0.205	0.21

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
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.271
f_angle_d	1.065
f_chiral_restr	0.051
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2944
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	74

Software

Software
Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.