9DRE

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ADP bound, P21 form)

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 1 21 1
Unit cell lengths	92.873, 80.109, 115.834
Unit cell angles	90.00, 90.12, 90.00

Refinement procedure

Resolution	49.190 - 1.690
R-factor	0.1771
Rwork	0.175
R-free	0.21050
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.009
RMSD bond angle	1.117
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]	49.190	1.730
High resolution limit [Å]	1.690	1.690
Rmerge	0.076	1.152
Rmeas	0.082	1.247
Rpim	0.031	0.473
Total number of observations	1301132	95728
Number of reflections	189816	13969
<I/σ(I)>	11.5	1.7
Completeness [%]	99.9
Redundancy	6.9	6.9
CC(1/2)	0.998	0.772

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 ADP, Puck: PSL-1501, Cryo: 30% (v/v) PEG 3350, 0.2 M sodium acetate, 0.1 M Tris 8.4.