6XDV

Self-assembly of a 3D DNA crystal lattice (4x5 junction version) containing the J3 immobile Holliday junction

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 19-ID
Synchrotron site	APS
Beamline	19-ID
Temperature [K]	100
Detector technology	PIXEL
Collection date	2018-03-15
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	0.92
Spacegroup name	P 32
Unit cell lengths	68.932, 68.932, 60.748
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	34.466 - 3.003
R-factor	0.2295
Rwork	0.227
R-free	0.25240
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	6x8c
RMSD bond length	0.007
RMSD bond angle	0.765
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	3.050
High resolution limit [Å]	3.000	8.130	3.000
Rmerge	0.098	0.078	0.621
Rmeas	0.103	0.082	0.659
Rpim	0.032	0.027	0.212
Number of reflections	6381	324	283
<I/σ(I)>	8
Completeness [%]	99.1	98.8	90.4
Redundancy	10.1	10.6	8.1
CC(1/2)	1.000	0.998	0.938

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		298	0.5 mL of 0.05 M Cacodylate pH 7.0 with 20 mM MgCl2, 1.0 mM spermine, 1.0 mM CoH18N6, and 15% Ethanol was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock