9DN3

Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-kinase (ITPK1) in Complex with an Inhibitor 9-cylcopentyladenine

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	2023-11-05
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.920072
Spacegroup name	P 21 21 21
Unit cell lengths	39.592, 60.244, 115.467
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	33.090 - 2.250
R-factor	0.2229
Rwork	0.219
R-free	0.27090
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.004
RMSD bond angle	0.721
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHASER
Refinement software	PHENIX (1.18.2_3874: ???)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	50.000	1.980
High resolution limit [Å]	1.950	1.950
Rmerge	0.102	0.777
Rmeas	0.108	0.816
Rpim	0.034	0.245
Number of reflections	19525	962
<I/σ(I)>	19.3	2.43
Completeness [%]	99.7	100
Redundancy	10.1	10.7
CC(1/2)	0.951	0.826

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP		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)