1IXJ
Crystal Structure of d(GCGAAAGCT) Containing Parallel-stranded Duplex with Homo Base Pairs and Anti-Parallel Duplex with Watson-Crick Base pairs
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | PHOTON FACTORY BEAMLINE BL-18B |
| Synchrotron site | Photon Factory |
| Beamline | BL-18B |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2000-12-08 |
| Detector | ADSC QUANTUM 4 |
| Wavelength(s) | 1.00 |
| Spacegroup name | I 41 2 2 |
| Unit cell lengths | 53.400, 53.400, 54.000 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 9.000 - 2.500 |
| Rwork | 0.215 |
| R-free | 0.25700 |
| Structure solution method | MAD |
| RMSD bond length | 0.005 |
| RMSD bond angle | 1.300 * |
| Data reduction software | MOSFLM |
| Data scaling software | SCALA |
| Phasing software | SOLVE |
| Refinement software | CNS |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 27.000 * | 2.520 |
| High resolution limit [Å] | 2.400 | 2.400 |
| Rmerge | 0.068 | 0.054 * |
| Total number of observations | 20224 * | |
| Number of reflections | 1647 * | |
| <I/σ(I)> | 2.7 | |
| Completeness [%] | 98.3 * | 100 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | 2,6-diaminopyridine, magnesium chloride, sodium chloride, hexaamminecobalt(III) chloride, 2-methyl-2,4-pentanediol, MEGA-10, sodium cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | 2,6-diaminopyridine, magnesium chloride, sodium chloride, hexaamminecobalt(III) chloride, 2-methyl-2,4-pentanediol, MEGA-10, sodium cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | 2,6-diaminopyridine | ||
| 2 | 1 | 1 | MgCl2 | ||
| 3 | 1 | 1 | NaCl | ||
| 4 | 1 | 1 | hexaamminecobalt(III) chloride | ||
| 5 | 1 | 1 | 2-methyl-2,4-pentanediol | ||
| 6 | 1 | 1 | MEGA-10 | ||
| 7 | 1 | 1 | sodium cacodylate |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | DNA | 3 (mM) | |
| 2 | 1 | drop | 2,6-diaminopyridine | 24 (mM) | |
| 3 | 1 | reservoir | 20 (mM) | pH6.0 | |
| 4 | 1 | reservoir | 80 (mM) | ||
| 5 | 1 | reservoir | 30 (mM) | ||
| 6 | 1 | reservoir | MPD | 25 (%) | |
| 7 | 1 | reservoir | n-decanoyl-N-methylglucamide | 0.17 (%) | |
| 8 | 1 | reservoir | sodium cacodylate | 40 (mM) |
