8E5E

Crystal structure of double-stranded DNA deaminase toxin DddA in complex with DNA with the target cytosine flipped into the active site

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 X 16M
Wavelength(s)	0.979180
Spacegroup name	P 61 2 2
Unit cell lengths	62.950, 62.950, 237.078
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	35.780 - 2.620
R-factor	0.2428
Rwork	0.242
R-free	0.25800
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6u08
RMSD bond angle	23.112
Data reduction software	XDS
Data scaling software	Aimless (0.5.32)
Phasing software	PHASER
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	44.870	2.740
High resolution limit [Å]	2.620	2.620
Rmerge	0.150	1.762
Rmeas	0.171	1.904
Rpim	0.079	0.706
Total number of observations	50693	7585
Number of reflections	8887	1076
<I/σ(I)>	45.6	1.4
Completeness [%]	98.0
Redundancy	5.7	7
CC(1/2)	0.979	0.589

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 25 % polyethylene glycol 3350