7JKG

Self-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the J3 immobile Holliday junction with R3 symmetry

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ALS BEAMLINE 5.0.2
Synchrotron site	ALS
Beamline	5.0.2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-09-15
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	1
Spacegroup name	H 3
Unit cell lengths	112.212, 112.212, 50.989
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	32.393 - 2.851
R-factor	0.212
Rwork	0.211
R-free	0.23470
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5vy6
RMSD bond length	0.008
RMSD bond angle	0.821
Data reduction software	HKL-2000
Data scaling software	HKL-2000
Phasing software	PHASER
Refinement software	PHENIX (1.11.1_2575)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.900
High resolution limit [Å]	2.850	7.730	2.850
Rmerge	0.088	0.095	1.044
Rmeas	0.093	0.099	1.104
Rpim	0.028	0.030	0.355
Total number of observations	57963
Number of reflections	5596	285	290
<I/σ(I)>	8.4
Completeness [%]	100.0	100	100
Redundancy	10.4	10.6	9.2
CC(1/2)		0.997	0.820

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		298	0.5 mL of 0.05 M Cacodylate pH 6.0 with 20 mM MgCl2, 1.0 mM spermine, 2 mM CaCl2, and 10% MPD was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock