6WOI

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 1-Diphosphoinositol pentakisphosphate, Mg, and Fluoride ion, presoaked with 1,5-IP8, Mg and Fluoride for 30 seconds

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 22-ID
Synchrotron site	APS
Beamline	22-ID
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-07-10
Detector	DECTRIS EIGER X 16M
Wavelength(s)	1.0
Spacegroup name	P 21 21 21
Unit cell lengths	46.503, 59.608, 62.353
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	31.630 - 1.500
R-factor	0.146
Rwork	0.145
R-free	0.16730
Structure solution method	FOURIER SYNTHESIS
RMSD bond length	0.011
RMSD bond angle	1.826
Data reduction software	DENZO
Data scaling software	SCALEPACK
Phasing software	PHASER
Refinement software	REFMAC (5.8.0253)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	1.530
High resolution limit [Å]	1.500	4.070	1.500
Rmerge	0.068	0.029	0.562
Rmeas	0.073	0.031	0.602
Rpim	0.024	0.010	0.207
Total number of observations	237334
Number of reflections	28143	1521	1359
<I/σ(I)>	10.5
Completeness [%]	99.0	96.8	97.1
Redundancy	8.4	9.1	7.3
CC(1/2)		0.998	0.905

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7	293	10% (w/v) PEG 8000, 10% (v/v) isopropanol, 200 mM Li2SO4, 75 mM NaAc, pH 5.5 and 25 mM HEPES, pH 7.0 and soaking in solution 400 mM LiCl, 30% (w/v) PEG 8000, 20% (v/v) isopropanol, 100mM NaAc, pH 4.5, 20 mM MgCl2 and 80 mM NaF in present of 2mM 1,5-IP8, and transferred into 400 mM LiCl, 30% (w/v) PEG 8000, 20% (v/v) isopropanol, 100mM HEPES, pH 7.0, 20 mM MgCl2 and 80 mM NaF for 30 second.