6WQG
Self-assembly of a 3D DNA crystal lattice (4x5 duplex 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) | 1.0 |
| 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 | 0.2347 |
| Rwork | 0.233 |
| R-free | 0.25050 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5kek |
| RMSD bond length | 0.006 |
| RMSD bond angle | 0.820 |
| 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 |
| Total number of observations | 64132 | ||
| 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, 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 |
