1R3E
Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit
Experimental procedure
| Experimental method | MAD |
| Source type | SYNCHROTRON |
| Source details | ALS BEAMLINE 8.3.1 |
| Synchrotron site | ALS |
| Beamline | 8.3.1 |
| Temperature [K] | 298 |
| Detector technology | CCD |
| Collection date | 2002-07-05 |
| Detector | ADSC QUANTUM 4 |
| Wavelength(s) | 0.9730, 0.9796, 0.9800, 1.1271 |
| Spacegroup name | C 1 2 1 |
| Unit cell lengths | 98.862, 159.337, 44.545 |
| Unit cell angles | 90.00, 97.77, 90.00 |
Refinement procedure
| Resolution | 40.000 * - 2.100 |
| R-factor | 0.223 |
| Rwork | 0.223 |
| R-free | 0.27300 |
| Structure solution method | MAD |
| RMSD bond length | 0.006 |
| RMSD bond angle | 1.360 |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | CNS |
| Refinement software | CNS |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 15.000 | 2.180 |
| High resolution limit [Å] | 2.100 | 2.100 |
| Rmerge | 0.076 | 0.731 * |
| Total number of observations | 525236 * | |
| Number of reflections | 38642 | |
| <I/σ(I)> | 15 | |
| Completeness [%] | 98.4 | 97.5 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | Vapor diffusion * | 7.5 * | ammonium sulfate, magnesium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | ammonium sulfate | ||
| 2 | 1 | 1 | magnesium sulfate | ||
| 3 | 1 | 1 | sodium cacodylate | ||
| 4 | 1 | 1 | H2O | ||
| 5 | 1 | 2 | ammonium sulfate | ||
| 6 | 1 | 2 | magnesium sulfate | ||
| 7 | 1 | 2 | sodium cacodylate | ||
| 8 | 1 | 2 | H2O |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | protein | 2.5 (mg/ml) | |
| 2 | 1 | drop | Tris | 10 (mM) | pH7.5 |
| 3 | 1 | drop | EDTA | 2 (mM) | |
| 4 | 1 | drop | dithiothreitol | 2 (mM) | |
| 5 | 1 | reservoir | 1.9 (M) | ||
| 6 | 1 | reservoir | 5 (mM) | ||
| 7 | 1 | reservoir | 100 (mM) | pH6.5 |
