7JNJ
Self-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the J26 immobile Holliday junction with R3 symmetry
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 | 2019-08-15 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 1 |
Spacegroup name | H 3 |
Unit cell lengths | 112.088, 112.088, 51.133 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 45.240 - 3.015 |
R-factor | 0.2105 |
Rwork | 0.207 |
R-free | 0.23610 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5vy6 |
RMSD bond length | 0.008 |
RMSD bond angle | 0.811 |
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 | 0.158 | 0.111 | 1.184 |
Rmeas | 0.166 | 0.117 | 1.283 |
Rpim | 0.053 | 0.036 | 0.475 |
Total number of observations | 37394 | ||
Number of reflections | 4461 | 235 | 147 |
<I/σ(I)> | 4.3 | ||
Completeness [%] | 94.9 | 100 | 64.2 |
Redundancy | 8.4 | 11 | 5.3 |
CC(1/2) | 0.986 | 0.525 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 298 | 0.5 mL of 0.05 M HEPES pH 7.5 with 15 mM MgCl2, 1.0 mM spermidine, and 10% dioxane was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock |