6XFZ
Self-assembly of a 3D DNA crystal lattice (4x5 junction version) containing the J29 immobile Holliday junction
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 | 2019-08-15 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 1 |
Spacegroup name | P 32 |
Unit cell lengths | 68.652, 68.652, 58.140 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 26.468 - 3.113 |
R-factor | 0.2458 |
Rwork | 0.244 |
R-free | 0.26220 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6x8c |
RMSD bond length | 0.005 |
RMSD bond angle | 0.673 |
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 | 3.150 |
High resolution limit [Å] | 3.100 | 8.400 | 3.100 |
Rmerge | 0.162 | 0.156 | 0.504 |
Rmeas | 0.170 | 0.164 | 0.538 |
Rpim | 0.053 | 0.051 | 0.182 |
Number of reflections | 4640 | 277 | 121 |
<I/σ(I)> | 4.7 | ||
Completeness [%] | 84.3 | 100 | 51.3 |
Redundancy | 9.3 | 10.5 | 7.1 |
CC(1/2) | 1.000 | 0.990 | 0.943 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 298 | 0.5 mL of 0.05 M HEPES pH 7.5 with 20 mM MgCl2, 1.0 mM spermine, and 5% PEG 8000 was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock |