9DUA

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (GMP 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	57.545, 80.309, 91.667
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	60.410 - 1.400
R-factor	0.1599
Rwork	0.158
R-free	0.18840
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.006
RMSD bond angle	0.853
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((1.21_5207: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	91.670	1.440
High resolution limit [Å]	1.400	1.400
Rmerge	0.072	1.151
Rmeas	0.075	1.233
Rpim	0.021	0.428
Total number of observations	1020007	35427
Number of reflections	81473	4551
<I/σ(I)>	17.6	1.7
Completeness [%]	96.8
Redundancy	12.5	7.8
CC(1/2)	0.999	0.626

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.4	291	20% (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 5mM GMP, Puck: PSL-0801, Cryo: 30% (v/v) PEG 3350, 0.2 M sodium acetate, 0.1 M Tris 8.4.