6WOF

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with inositol hexakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 20min in the absence of Fluoride.

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	2019-07-11
Detector	DECTRIS EIGER X 16M
Wavelength(s)	1.0
Spacegroup name	P 21 21 21
Unit cell lengths	46.062, 59.827, 62.729
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	27.790 - 1.600
R-factor	0.1239
Rwork	0.123
R-free	0.14840
Structure solution method	FOURIER SYNTHESIS
RMSD bond length	0.007
RMSD bond angle	1.550
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	1.630
High resolution limit [Å]	1.600	4.340	1.600
Rmerge	0.048	0.034	0.235
Rmeas	0.051	0.036	0.248
Rpim	0.016	0.011	0.078
Total number of observations	200552
Number of reflections	22702	1210	1138
<I/σ(I)>	11.9
Completeness [%]	97.3	93.1	99.6
Redundancy	8.8	9.2	8.9
CC(1/2)		0.999	0.989

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 of 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM HEPES, pH 7.0, 80 mM NaF, 20 mM MgCl2 in present of 2mM 5-IP7 for 2 days, and transferred into 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM HEPES, pH 7.0, 20 mM MgCl2 for 20 min.