9ZWS

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

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	2024-06-20
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.97857
Spacegroup name	I 2 2 2
Unit cell lengths	104.138, 107.156, 113.983
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	74.680 - 2.000
R-factor	0.1832
Rwork	0.182
R-free	0.21390
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	0.823
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]	78.130	2.070
High resolution limit [Å]	2.000	2.000
Rmerge	0.093	0.093
Rmeas	0.097	1.892
Rpim	0.027	0.503
Number of reflections	43332	4260
<I/σ(I)>	18
Completeness [%]	100.0
Redundancy	13.6
CC(1/2)	0.998	0.672

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 ACA.