6WOD

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with inositol hexakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 2min 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	2019-07-10
Detector	DECTRIS EIGER X 16M
Wavelength(s)	1.0
Spacegroup name	P 21 21 21
Unit cell lengths	46.224, 59.605, 62.719
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	27.770 - 1.350
R-factor	0.1339
Rwork	0.133
R-free	0.15640
Structure solution method	FOURIER SYNTHESIS
RMSD bond length	0.009
RMSD bond angle	1.681
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	1.370
High resolution limit [Å]	1.350	3.660	1.350
Rmerge	0.044	0.028	0.415
Rmeas	0.046	0.029	0.440
Rpim	0.015	0.009	0.142
Total number of observations	354211
Number of reflections	37995	2093	1653
<I/σ(I)>	12
Completeness [%]	98.4	98.9	87.4
Redundancy	9.3	9.2	8.3
CC(1/2)		0.999	0.962

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 2min.