7JOJ
Self-assembly of a 3D DNA crystal lattice (4x6 duplex version) containing the J28 immobile Holliday junction
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | NSLS-II BEAMLINE 17-ID-1 |
| Synchrotron site | NSLS-II |
| Beamline | 17-ID-1 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2017-07-15 |
| Detector | DECTRIS EIGER X 9M |
| Wavelength(s) | 0.92 |
| Spacegroup name | P 32 |
| Unit cell lengths | 67.903, 67.903, 59.509 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 33.952 - 3.108 |
| R-factor | 0.1945 |
| Rwork | 0.193 |
| R-free | 0.22300 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5vy6 |
| RMSD bond length | 0.007 |
| RMSD bond angle | 0.735 |
| 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 | 0.153 | 0.101 | 0.548 |
| Rmeas | 0.163 | 0.108 | 0.585 |
| Rpim | 0.054 | 0.036 | 0.200 |
| Total number of observations | 43008 | ||
| Number of reflections | 4995 | 277 | 167 |
| <I/σ(I)> | 4.6 | ||
| Completeness [%] | 90.3 | 100 | 63.5 |
| Redundancy | 8.6 | 11.1 | 6.1 |
| CC(1/2) | 0.948 | 0.962 |
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 1.0 mM spermine, 2.0 mM CoH18N6, 30 mM CaCl2, and 2.0 M LiCl was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock |
