8E5D

Crystal structure of double-stranded DNA deaminase toxin DddA in complex with DNA with the target cytosine parked in the major groove

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 24-ID-C
Synchrotron site	APS
Beamline	24-ID-C
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-06-21
Detector	DECTRIS EIGER2 S 16M
Wavelength(s)	0.979180
Spacegroup name	P 2 2 21
Unit cell lengths	31.699, 94.611, 138.465
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	44.770 - 2.390
R-factor	0.1997
Rwork	0.198
R-free	0.23260
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6u08
RMSD bond angle	25.812
Data reduction software	XDS
Data scaling software	Aimless (0.7.7)
Phasing software	PHASER
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	47.150	2.550
High resolution limit [Å]	2.390	2.390
Rmerge	0.092	1.139
Rmeas	0.101	1.240
Rpim	0.042	0.485
Number of reflections	13177	659
<I/σ(I)>	5.1	1.8
Completeness [%]	93.2
Redundancy	5.1
CC(1/2)	0.998	0.804

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M sodium dihydrogen phosphate, 20 % polyethylene glycol 3350