9DRF

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (DTP bound, P21 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	2024-03-24
Detector	DECTRIS EIGER2 XE 9M
Wavelength(s)	0.9786
Spacegroup name	P 1 21 1
Unit cell lengths	93.034, 80.131, 116.189
Unit cell angles	90.00, 90.13, 90.00

Refinement procedure

Resolution	49.230 - 1.780
R-factor	0.1808
Rwork	0.179
R-free	0.21750
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.010
RMSD bond angle	1.048
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((dev_5295: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	49.230	1.830
High resolution limit [Å]	1.780	1.780
Rmerge	0.068	1.136
Rmeas	0.073	1.228
Rpim	0.028	0.462
Total number of observations	1115757	83689
Number of reflections	163324	11978
<I/σ(I)>	12.6	1.7
Completeness [%]	99.9
Redundancy	6.8	7
CC(1/2)	0.999	0.787

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 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTP), Puck: PSL-1510, Cryo: 30% (v/v) PEG 3350, 0.2 M sodium acetate, 0.1 M Tris 8.4.