9DU9

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (GDP/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	57.437, 79.552, 91.796
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	48.690 - 1.350
R-factor	0.1581
Rwork	0.157
R-free	0.18710
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.005
RMSD bond angle	0.870
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]	48.690	1.370
High resolution limit [Å]	1.350	1.350
Rmerge	0.057	0.834
Rmeas	0.059	0.872
Rpim	0.016	0.246
Total number of observations	1212900	43472
Number of reflections	89405	3693
<I/σ(I)>	26.5	3.3
Completeness [%]	96.4
Redundancy	13.6	11.8
CC(1/2)	1.000	0.730

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 GDP and 5mM MgCl2, Puck: PSL-0209, Cryo: 30% (v/v) PEG 3350, 0.2 M sodium acetate, 0.1 M Tris 8.5.