9B21

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ADP Ribose bound, Orthorhombic P 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	2024-02-10
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 21 21 21
Unit cell lengths	57.365, 78.788, 91.564
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	48.610 - 1.600
R-factor	0.1653
Rwork	0.164
R-free	0.19560
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.009
RMSD bond angle	1.010
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]	48.610	1.640
High resolution limit [Å]	1.600	1.600
Rmerge	0.107	1.954
Rmeas	0.111	2.035
Rpim	0.031	0.560
Number of reflections	55537	4056
<I/σ(I)>	13	1.5
Completeness [%]	100.0	100
Redundancy	13	12.8
CC(1/2)	0.999	0.629

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	26% 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 ADP-ribose. Electron density consistent with the alpha-D-ribose form. plate Liu-S-102, D6. Puck: PSL-1005, Cryo: 33% PEG 4000.