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 |