9DT7

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (5-O-phosphono-alpha-D-ribofuranose 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	2024-03-24
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 21 21 21
Unit cell lengths	57.509, 79.740, 91.709
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	60.170 - 1.150
R-factor	0.1313
Rwork	0.130
R-free	0.15250
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.010
RMSD bond angle	1.190
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]	91.710	1.180
High resolution limit [Å]	1.150	1.150
Rmerge	0.049	0.477
Rmeas	0.051	0.609
Rpim	0.014	0.369
Total number of observations	1379941	3948
Number of reflections	127124	1749
<I/σ(I)>	21.8	1.7
Completeness [%]	84.8
Redundancy	10.9	2.3
CC(1/2)	1.000	0.773

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 5-O-phosphono-alpha-D-ribofuranose (HSX), Puck: PSL-1603, Cryo: 30% (v/v) PEG 3350, 0.2 M sodium acetate, 0.1 M Tris 8.4.