13LZ

Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-kinase (ITPK1) in Complex with an Inhibitor NCGC00879727

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 17-ID-1
Synchrotron site	NSLS-II
Beamline	17-ID-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-11-17
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.97934
Spacegroup name	P 1 21 1
Unit cell lengths	39.757, 126.219, 63.029
Unit cell angles	90.00, 90.12, 90.00

Refinement procedure

Resolution	33.660 - 2.200
R-factor	0.2165
Rwork	0.215
R-free	0.25020
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.002
RMSD bond angle	0.500
Data reduction software	AutoProcess
Data scaling software	AutoProcess
Phasing software	PHENIX
Refinement software	PHENIX (1.21.2)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	33.660	2.240
High resolution limit [Å]	2.200	2.200
Rmerge	0.127	1.224
Rmeas	0.153	1.477
Rpim	0.083	0.818
Number of reflections	31194	1526
<I/σ(I)>	6.1	1
Completeness [%]	99.1	99.1
Redundancy	3.2	3.1
CC(1/2)	0.993	0.318

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	8	298	Hanging drops comprised 2 ul of 14 mg/mL protein solution and 2 ul of well buffer (21% (w/v) PEG 8000, 0.17 mM (NH4)2SO4, 85 mM Tris-HCl, pH 8.0, and 10% Glycerol) that was present in the reservoir. Crystal complexes with inhibitors were formed in a soaking buffer (25% (w/v) PEG 8000, 0.17 mM (NH4)2SO4, 85 mM Tris-HCl, pH 8.0, 20% Glycerol)