9DSZ

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (DTP 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 1 21 1
Unit cell lengths	92.843, 79.311, 115.827
Unit cell angles	90.00, 90.30, 90.00

Refinement procedure

Resolution	72.630 - 1.900
R-factor	0.198
Rwork	0.196
R-free	0.23340
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	0.870
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((dev_5396: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	92.840	1.950
High resolution limit [Å]	1.900	1.900
Rmerge	0.097	1.256
Rmeas	0.106	1.377
Rpim	0.043	0.556
Total number of observations	781765	57372
Number of reflections	132200	9727
<I/σ(I)>	10	1.6
Completeness [%]	99.8
Redundancy	5.9	5.9
CC(1/2)	0.998	0.695

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	20% (v/v) PEG 3350, 0.2M sodium acetate, 0.1 M Tris 8.5, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-107 AB/12. 5 hour soak in 5mM DTP/MgCl2, Puck: PSL-0206, Cryo: 30% (v/v) PEG 3350, 0.2 M sodium acetate, 0.1 M Tris 8.5.