9ZWT

Crystal structure of the N4BP2 polynucleotide kinase domain complexed with ATP or ADP, Mg, and the trinucleotide substrate AGA or its 5'-phosphorylated product pAGA.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 17-ID-1
Synchrotron site	NSLS-II
Beamline	17-ID-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-08-08
Detector	DECTRIS EIGER2 S 9M
Wavelength(s)	0.920105
Spacegroup name	I 2 2 2
Unit cell lengths	103.764, 106.150, 113.360
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	33.080 - 2.720
R-factor	0.1961
Rwork	0.193
R-free	0.26040
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.033
RMSD bond angle	0.771
Data reduction software	autoPROC
Data scaling software	autoPROC
Phasing software	PHASER
Refinement software	PHENIX (2.0_5936)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	33.080	2.760
High resolution limit [Å]	2.720	2.720
Rmerge	0.174	1.760
Rmeas	0.197	2.001
Rpim	0.127	0.887
Number of reflections	17181	852
<I/σ(I)>	6.6	1
Completeness [%]	99.8
Redundancy	4.5
CC(1/2)	0.993	0.334

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION		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 AGA.