7TN4

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 3-diphosphoinositol 1,2,4,5-tetrakisphosphate (3-PP-IP4), Mg and Fluoride ion

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	2021-02-26
Detector	DECTRIS EIGER X 16M
Wavelength(s)	1.0
Spacegroup name	P 21 21 21
Unit cell lengths	45.149, 59.743, 62.769
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	31.400 - 1.850
R-factor	0.1841
Rwork	0.182
R-free	0.21730
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6wo7
RMSD bond length	0.015
RMSD bond angle	1.936
Data reduction software	xia2
Data scaling software	SCALEPACK
Phasing software	PHASER
Refinement software	REFMAC (5.8.0238)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	1.880
High resolution limit [Å]	1.850	5.020	1.850
Rmerge	0.116	0.105	0.380
Rmeas	0.122	0.110	0.399
Rpim	0.036	0.033	0.122
Total number of observations	165071
Number of reflections	14853	836	726
<I/σ(I)>	8.4
Completeness [%]	99.5	99.5	98.4
Redundancy	11.1	11.7	9.9
CC(1/2)		0.987	0.982

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	5	293	10% w/v PEG8000, 10% v/v isopropanol, 200 mM lithium sulfate, 100 mM sodium acetate, pH 5.0, 5 mM IP6, soaked in 200 mM lithium chloride, 20% w/v PEG8000, 20% v/v isopropanol, 100 mM sodium acetate, pH 5.0, 20 mM magnesium chloride, 100 mM sodium fluoride in presence of ZmITPK1 reaction solution with 1,2,3,4,5-IP5