9DUD

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (FAD 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	2024-08-03
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 21 21 21
Unit cell lengths	57.351, 79.690, 91.973
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	60.230 - 1.320
R-factor	0.1448
Rwork	0.143
R-free	0.16960
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	1.020
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]	79.690	1.350
High resolution limit [Å]	1.320	1.320
Rmerge	0.066	1.276
Rmeas	0.068	1.361
Rpim	0.019	0.462
Total number of observations	1263006	54225
Number of reflections	98710	6630
<I/σ(I)>	18.1	1.6
Completeness [%]	99.2
Redundancy	12.8	8.2
CC(1/2)	0.999	0.642

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. plaate Liu-S-107 AB/12 ApoSoak. 5 hour soak in 8mM FAD. Nicotinamide portion of FAD is disordered Puck: PSL-2109, Cryo: 30% (v/v) PEG 3350, 0.2 M sodium acetate, 0.1 M Tris 8.5.