1NJM
The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycin
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 19-ID |
| Synchrotron site | APS |
| Beamline | 19-ID |
| Temperature [K] | 90 |
| Detector technology | CCD |
| Collection date | 2001-11-09 |
| Detector | CUSTOM-MADE |
| Spacegroup name | I 2 2 2 |
| Unit cell lengths | 169.600, 409.400, 695.100 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 15.000 - 3.600 |
| R-factor | 0.2841 |
| Rwork | 0.284 |
| R-free | 0.32600 * |
| Structure solution method | DIFFERENCE FOURIER MAPS |
| Starting model (for MR) | 1nkw |
| RMSD bond length | 0.005 * |
| RMSD bond angle | 0.970 * |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | CCP4 |
| Refinement software | CNS |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 50.000 | 3.660 |
| High resolution limit [Å] | 3.600 | 3.600 |
| Rmerge | 0.169 * | 0.356 * |
| Number of reflections | 290998 | |
| <I/σ(I)> | 5.8 | 1.7 |
| Completeness [%] | 95.2 * | 93.8 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | Vapor diffusion * | 7.8 * | 18 * | Harms, J.M., (2001) Cell (Cambridge,Mass.), 107, 679. * |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | ETHANOL | ||
| 10 | 1 | 2 | MGCL2 | ||
| 11 | 1 | 2 | KCL | ||
| 12 | 1 | 2 | NH4CL | ||
| 2 | 1 | 1 | DIMETHYLHEXANEDIOL | ||
| 3 | 1 | 1 | MGCL2 | ||
| 4 | 1 | 1 | KCL | ||
| 5 | 1 | 1 | NH4CL | ||
| 6 | 1 | 1 | SPARSOMYCIN | ||
| 7 | 1 | 1 | HEPES | ||
| 8 | 1 | 2 | ETHANOL | ||
| 9 | 1 | 2 | DIMETHYLHEXANEDIOL |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | reservoir | 10 (mM) | ||
| 2 | 1 | reservoir | 60 (mM) | ||
| 3 | 1 | reservoir | 5 (mM) | ||
| 4 | 1 | reservoir | HEPES | 10 (mM) | pH7.8 |
