9DU8

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ADP/Mg 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	2024-04-13
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 21 21 21
Unit cell lengths	57.375, 79.335, 91.822
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	48.660 - 1.350
R-factor	0.1441
Rwork	0.143
R-free	0.16870
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	1.159
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((dev_5449: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	48.660	1.370
High resolution limit [Å]	1.350	1.350
Rmerge	0.054	0.891
Rmeas	0.056	0.943
Rpim	0.016	0.304
Total number of observations	1201489	41795
Number of reflections	92588	4471
<I/σ(I)>	23.4	2.6
Completeness [%]	99.9
Redundancy	13	9.3
CC(1/2)	1.000	0.826

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 8.5, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-107 AB/12. 5 hour soak in 5mM ADP and 5mM MgCl2, Puck: PSL-0201, Cryo: 30% (v/v) PEG 3350, 0.2 M sodium acetate, 0.1 M Tris 8.5.