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 |