9DU6

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ATP bound)

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	2024-03-03
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 21 21 21
Unit cell lengths	57.934, 80.392, 92.888
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	49.160 - 1.550
R-factor	0.1737
Rwork	0.172
R-free	0.20240
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.009
RMSD bond angle	1.026
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((dev_5295: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	49.160	1.580
High resolution limit [Å]	1.550	1.550
Rmerge	0.064	1.296
Rmeas	0.067	1.347
Rpim	0.018	0.362
Total number of observations	853652	42533
Number of reflections	63707	3113
<I/σ(I)>	18.2	2.1
Completeness [%]	100.0
Redundancy	13.4	13.7
CC(1/2)	0.999	0.813

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	25% (v/v) PEG 3350, 0.2M sodium acetate, 0.1 M Tris 8.4, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-107 CD/34. 5 hour soak in 2mM ATP, Puck: PSL-1504, Cryo: 30% (v/v) PEG 3350, 0.2 M sodium acetate, 0.1 M Tris 8.4.