9B22

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ADP Ribose and AMP 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	2024-02-10
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 1 21 1
Unit cell lengths	39.826, 92.659, 57.716
Unit cell angles	90.00, 91.68, 90.00

Refinement procedure

Resolution	36.580 - 1.300
R-factor	0.1378
Rwork	0.137
R-free	0.16350
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	1.019
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((dev_5243: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	36.580	1.330
High resolution limit [Å]	1.300	1.300
Rmerge	0.056	0.692
Rmeas	0.061	0.793
Rpim	0.023	0.377
Total number of observations	641274	25108
Number of reflections	100227	6043
<I/σ(I)>	14.3	1.7
Completeness [%]	97.7
Redundancy	6.4	4.2
CC(1/2)	0.999	0.695

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	23% PEG 4000, 0.1M Tris, pH 8.5, 0.2 M sodium acetate, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. 3 minutue soak in 15 mM AMP and 15 mM ADP-ribose. Electron density consistent with the alpha-D-ribose form. Subunit B contains AMP and ADP-ribose in the active site and were refined with grouped occupancies. plate Liu-S-102, F8. Puck: PSL-1011, Cryo: 10% extra PEG 4000 added to the drop.