9DTC

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ADP Ribose bound, orthrhombic form2)

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 21 21 21
Unit cell lengths	57.426, 79.749, 91.982
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	48.710 - 1.400
R-factor	0.1636
Rwork	0.162
R-free	0.18810
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	1.084
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]	48.710	1.420
High resolution limit [Å]	1.400	1.400
Rmerge	0.074	1.407
Rmeas	0.078	1.488
Rpim	0.024	0.474
Total number of observations	848621	38864
Number of reflections	83201	4068
<I/σ(I)>	16.6	1.6
Completeness [%]	99.5
Redundancy	10.2	9.6
CC(1/2)	0.999	0.594

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-1006, Cryo: 10% extra PEG 4000 added to the drop.