1YZD
Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | ROTATING ANODE |
| Source details | RIGAKU |
| Temperature [K] | 100 |
| Detector technology | IMAGE PLATE |
| Collection date | 2004-02-24 |
| Detector | RIGAKU RAXIS IV++ |
| Spacegroup name | P 31 2 1 |
| Unit cell lengths | 43.000, 43.000, 121.000 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 8.070 - 2.350 |
| R-factor | 0.236 |
| Rwork | 0.236 |
| R-free | 0.29200 |
| Structure solution method | MOLECULAR REPLACEMENT |
| RMSD bond length | 0.005 |
| RMSD bond angle | 0.900 |
| Data reduction software | CrystalClear ((MSC/RIGAKU)) |
| Data scaling software | SCALEPACK |
| Phasing software | AMoRE |
| Refinement software | CNS (1.1) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 31.700 | 2.280 |
| High resolution limit [Å] | 2.180 | 2.180 |
| Rmerge | 0.077 | 0.387 |
| Number of reflections | 6646 | |
| <I/σ(I)> | 15.2 | 3.37 |
| Completeness [%] | 91.4 | 57.4 |
| Redundancy | 21.79 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8 | 273 | MPD, sodium cacodylate, spermidine, magnesium chloride, calcium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | MPD | ||
| 10 | 1 | 2 | calcium chloride | ||
| 2 | 1 | 1 | sodium cacodylate | ||
| 3 | 1 | 1 | spermidine | ||
| 4 | 1 | 1 | magnesium chloride | ||
| 5 | 1 | 1 | calcium chloride | ||
| 6 | 1 | 1 | H2O | ||
| 7 | 1 | 2 | MPD | ||
| 8 | 1 | 2 | sodium cacodylate | ||
| 9 | 1 | 2 | magnesium chloride |
