1QDA
Crystal structure of epidoxorubicin-formaldehyde virtual crosslink of DNA
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | ROTATING ANODE |
| Source details | RIGAKU RU200 |
| Temperature [K] | 298 |
| Detector technology | IMAGE PLATE |
| Collection date | 1998-01-23 |
| Detector | RIGAKU RAXIS II |
| Spacegroup name | P 41 21 2 |
| Unit cell lengths | 28.110, 28.110, 52.540 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 30.000 - 1.600 |
| R-factor | 0.2052 |
| Rwork | 0.205 |
| R-free | 0.26780 |
| RMSD bond length | 0.020 |
| RMSD bond angle | 2.100 |
| Data scaling software | SCALEPACK |
| Phasing software | CNS |
| Refinement software | CNS |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 1.660 |
| High resolution limit [Å] | 1.600 | 1.600 |
| Rmerge | 0.099 | 0.309 |
| Total number of observations | 47174 * | |
| Number of reflections | 3101 | 2482 * |
| <I/σ(I)> | 6.8 | |
| Completeness [%] | 92.0 | 82.7 |
| Redundancy | 12 | 9.5 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6 | 296 | MPD, FORMALDEHYDE, CACODYLATE, SPERMINE, BARIUM CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | FORMALDEHYDE | ||
| 2 | 1 | 1 | SODIUM CACODYLATE | ||
| 3 | 1 | 1 | SPERMINE | ||
| 4 | 1 | 1 | BACL2 | ||
| 5 | 1 | 1 | MPD | ||
| 6 | 1 | 2 | MPD |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | d(CGCGCG) | 1.2 (mM) | |
| 2 | 1 | drop | epidoxorubicin | 1.2 (mM) | |
| 3 | 1 | drop | formaldehyde | 9 (mM) | |
| 4 | 1 | drop | sodium cacodylate | 30 (mM) | |
| 5 | 1 | drop | spermine | 16.1 (mM) | |
| 6 | 1 | drop | 4.4 (mM) | ||
| 7 | 1 | reservoir | MPD | 40 (%) |
