9ZX0

Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ADP, Mg, and 5'-phosphorylated GCA (pGCA).

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 19-ID
Synchrotron site	NSLS-II
Beamline	19-ID
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-07-24
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.97857
Spacegroup name	I 2 2 2
Unit cell lengths	104.186, 107.180, 114.871
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	35.940 - 2.450
R-factor	0.1745
Rwork	0.170
R-free	0.22780
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.014
RMSD bond angle	1.281
Data reduction software	XDS
Data scaling software	XDS
Phasing software	PHASER
Refinement software	PHENIX (2.0_5936)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	50.000	2.490
High resolution limit [Å]	2.450	2.450
Rmerge	0.103	0.673
Rmeas	0.116	0.787
Rpim	0.052	0.398
Number of reflections	23915	1190
<I/σ(I)>	16.4	2.23
Completeness [%]	99.6	99.4
Redundancy	4.8	3.8
CC(1/2)	0.990	0.591

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP		295	Crystals were grown in 20% PEG 3350, 0.2 M ammonium sulfate, 0.1 M MES/imidazole (pH 6.0), 100 mM Mg2+, 2 mM ATP, 10% isopropanol, and 5% PEG 400, and were soaked for 16 h in the same solution supplemented with 5 mM ATP and 1 mM GCA.