1P4Z
Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 14-BM-C |
Synchrotron site | APS |
Beamline | 14-BM-C |
Temperature [K] | 103 |
Detector technology | CCD |
Collection date | 2002-07-18 |
Detector | ADSC QUANTUM 4 |
Spacegroup name | P 61 2 2 |
Unit cell lengths | 33.380, 33.380, 87.670 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 20.000 * - 2.000 |
R-factor | 0.236 |
Rwork | 0.236 |
R-free | 0.26800 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | UNPUBLISHED RESULTS OF STRUCTURE WITH ISOMORPHOUS UNIT CELL DIMENSIONS |
RMSD bond length | 0.015 |
RMSD bond angle | 1.750 * |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | EPMR |
Refinement software | CNS (1.0) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 * | 2.130 |
High resolution limit [Å] | 2.000 | 2.000 |
Rmerge | 0.048 * | 0.124 |
Total number of observations | 32690 * | |
Number of reflections | 2143 | |
<I/σ(I)> | 2.38 | |
Completeness [%] | 94.6 * | 53.2 * |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | Vapor diffusion * | 7.5 | 20 * | 0.6mM DNA, 5mM TRIS(HCl), 25mM Ca-Acetate, 7% MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.50 |
Crystallization Reagents
ID | crystal ID | solution ID | reagent name | concentration | details |
1 | 1 | 1 | TRIS(HCl) | ||
2 | 1 | 1 | Ca-Acetate | ||
3 | 1 | 1 | MPD | ||
4 | 1 | 1 | H2O | ||
5 | 1 | 2 | Ca-Acetate | ||
6 | 1 | 2 | MPD | ||
7 | 1 | 2 | TRIS(HCl) | ||
8 | 1 | 2 | H2O |
Crystallization Reagents in Literatures
ID | crystal ID | solution | reagent name | concentration (unit) | details |
1 | 1 | drop | DNA | 0.6 (mM) | |
2 | 1 | drop | Tris-HCl | 5 (mM) | pH7.5 |
3 | 1 | drop | calcium acetate | 25 (mM) | |
4 | 1 | drop | MPD | 7 (%) | |
5 | 1 | reservoir | MPD | 30 (%) |