7JKG
Self-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the J3 immobile Holliday junction with R3 symmetry
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 | 2019-09-15 |
| Detector | DECTRIS PILATUS3 6M |
| Wavelength(s) | 1 |
| Spacegroup name | H 3 |
| Unit cell lengths | 112.212, 112.212, 50.989 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 32.393 - 2.851 |
| R-factor | 0.212 |
| Rwork | 0.211 |
| R-free | 0.23470 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5vy6 |
| RMSD bond length | 0.008 |
| RMSD bond angle | 0.821 |
| 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 | 2.900 |
| High resolution limit [Å] | 2.850 | 7.730 | 2.850 |
| Rmerge | 0.088 | 0.095 | 1.044 |
| Rmeas | 0.093 | 0.099 | 1.104 |
| Rpim | 0.028 | 0.030 | 0.355 |
| Total number of observations | 57963 | ||
| Number of reflections | 5596 | 285 | 290 |
| <I/σ(I)> | 8.4 | ||
| Completeness [%] | 100.0 | 100 | 100 |
| Redundancy | 10.4 | 10.6 | 9.2 |
| CC(1/2) | 0.997 | 0.820 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 298 | 0.5 mL of 0.05 M Cacodylate pH 6.0 with 20 mM MgCl2, 1.0 mM spermine, 2 mM CaCl2, and 10% MPD was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock |
