1P6V
Crystal structure of the tRNA domain of transfer-messenger RNA in complex with SmpB
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SLS BEAMLINE X06SA |
| Synchrotron site | SLS |
| Beamline | X06SA |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2002-11-12 |
| Detector | MARRESEARCH |
| Wavelength(s) | 1.008 |
| Spacegroup name | P 43 21 2 |
| Unit cell lengths | 99.680, 99.680, 207.050 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 20.000 * - 3.200 |
| R-factor | 0.302 |
| Rwork | 0.302 |
| R-free | 0.36000 |
| Structure solution method | MAD |
| RMSD bond length | 0.007 |
| RMSD bond angle | 22.200 * |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | SOLVE |
| Refinement software | CNS (1.1) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 3.300 |
| High resolution limit [Å] | 3.200 | 3.200 |
| Rmerge | 0.075 * | 0.873 * |
| Number of reflections | 17756 | |
| <I/σ(I)> | 23.1 | 2.4 |
| Completeness [%] | 98.4 | 100 |
| Redundancy | 6.9 | 7.3 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.8 | 19 * | Isopropanol, cacodylate, ammonium acetate, magnesium acetate, calcium acetate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | Isopropanol | ||
| 10 | 1 | 2 | H2O | ||
| 2 | 1 | 1 | cacodylate | ||
| 3 | 1 | 1 | ammonium acetate | ||
| 4 | 1 | 1 | magnesium acetate | ||
| 5 | 1 | 1 | calcium acetate | ||
| 6 | 1 | 1 | H2O | ||
| 7 | 1 | 2 | cacodylate | ||
| 8 | 1 | 2 | magnesium acetate | ||
| 9 | 1 | 2 | calcium acetate |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | protein | 6 (mg/ml) | |
| 2 | 1 | reservoir | 2-propanol | 10 (%) | |
| 3 | 1 | reservoir | magnesium acetate | 100 (mM) | |
| 4 | 1 | reservoir | ammonium acetate | 15 (mM) | |
| 5 | 1 | reservoir | sodium cacodylate | 50 (mM) | pH6.8 |
| 6 | 1 | reservoir | gentamicin | 0.2 (mM) | or neomycin B |
| 7 | 1 | reservoir | 16 (mM) |
