1S47
Crystal structure analysis of the DNA quadruplex d(TGGGGT)S2
Experimental procedure
| Experimental method | MAD |
| Source type | SYNCHROTRON |
| Source details | ESRF BEAMLINE BM14 |
| Synchrotron site | ESRF |
| Beamline | BM14 |
| Detector technology | CCD |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 28.319, 56.341, 51.746 |
| Unit cell angles | 90.00, 99.17, 90.00 |
Refinement procedure
| Resolution | 19.840 - 2.500 |
| R-factor | 0.224 |
| Rwork | 0.224 |
| R-free | 0.31300 * |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 1s45 |
| RMSD bond length | 0.004 |
| RMSD bond angle | 0.740 * |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | EPMR |
| Refinement software | CNS (1.1) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 20.000 | 2.590 |
| High resolution limit [Å] | 2.500 | 2.500 |
| Rmerge | 0.080 | 0.160 |
| Number of reflections | 10915 | |
| Completeness [%] | 98.3 * | 97.3 |
| Redundancy | 5.43 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | Vapor diffusion, hanging drop * | 6.5 | 4 * | PEG 400, sodium cacodylate, magnesium chloride, spermine, tetrahydrochlorhide, thallium acetate, lysine-anthraquinone, d(TGGGGT), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.50 |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | PEG 400 | ||
| 10 | 1 | 2 | magnesium chloride | ||
| 11 | 1 | 2 | thallium acetate | ||
| 12 | 1 | 2 | sodium cacodylate | ||
| 13 | 1 | 2 | H2O | ||
| 2 | 1 | 1 | sodium cacodylate | ||
| 3 | 1 | 1 | magnesium chloride | ||
| 4 | 1 | 1 | spermine | ||
| 5 | 1 | 1 | tetrahydrochlorhide | ||
| 6 | 1 | 1 | thallium acetate | ||
| 7 | 1 | 1 | lysine-anthraquinone | ||
| 8 | 1 | 1 | H2O | ||
| 9 | 1 | 2 | PEG 400 |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | sodium cacodylate | 20 (mM) | pH6.5 |
| 2 | 1 | drop | 30 (mM) | ||
| 3 | 1 | drop | spermine 4HCl | 1 (mM) | |
| 4 | 1 | drop | Thallium acetate | 0.25 (mM) | |
| 5 | 1 | drop | lysine-anthraquinone | 20000 (nM) | |
| 6 | 1 | drop | d(TGGGGT) | 0.5 (mM) | |
| 7 | 1 | drop | PEG400 | 2.5 (%(v/v)) | |
| 8 | 1 | reservoir | PEG400 | 25 (%(v/v)) |
