8T98

Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with Scyllo-3-PP-(1,2,4,5)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	2021-10-08
Detector	DECTRIS EIGER X 16M
Wavelength(s)	1.0
Spacegroup name	P 21 21 21
Unit cell lengths	46.103, 59.571, 62.430
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	36.490 - 1.300
R-factor	0.15033
Rwork	0.149
R-free	0.17181
Structure solution method	FOURIER SYNTHESIS
RMSD bond length	0.018
RMSD bond angle	2.175
Data reduction software	DENZO
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	1.320
High resolution limit [Å]	1.300	3.530	1.300
Rmerge	0.071	0.047	0.442
Rmeas		0.050	0.466
Rpim		0.016	0.143
Number of reflections	42475	2353	1775
<I/σ(I)>	7.1
Completeness [%]	98.0	99.6	82.8
Redundancy	10.2	9.6	9
CC(1/2)		0.998	0.939

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP		298	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 TvIPK reaction solution with scyllo-IP5