6XDW
Self-assembly of a 3D DNA crystal lattice (4x5 junction version) containing the J5 immobile Holliday junction
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 19-BM |
Synchrotron site | APS |
Beamline | 19-BM |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2017-12-15 |
Detector | ADSC QUANTUM 210r |
Wavelength(s) | 1 |
Spacegroup name | P 32 2 1 |
Unit cell lengths | 67.918, 67.918, 59.511 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 41.834 - 3.148 |
R-factor | 0.2259 |
Rwork | 0.224 |
R-free | 0.25990 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6x8c |
RMSD bond length | 0.012 |
RMSD bond angle | 1.231 |
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 | 3.200 |
High resolution limit [Å] | 3.148 | 8.540 | 3.150 |
Rmerge | 0.149 | 0.035 | 0.641 |
Rmeas | 0.156 | 0.037 | 0.678 |
Rpim | 0.044 | 0.012 | 0.209 |
Number of reflections | 2891 | 165 | 120 |
<I/σ(I)> | 5.4 | ||
Completeness [%] | 98.0 | 97.1 | 82.8 |
Redundancy | 12.3 | 11.7 | 7.3 |
CC(1/2) | 1.000 | 0.997 | 0.882 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 298 | 0.5 mL of 0.05 M Cacodylate pH 6.5 with 36 mM MgCl2, 2.25 mM spermine, and 5% PEG 400 was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock |