1SI7
Structure of E. coli tRNA psi 13 pseudouridine synthase TruD
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | NSLS BEAMLINE X12C |
Synchrotron site | NSLS |
Beamline | X12C |
Temperature [K] | 93 |
Detector technology | CCD |
Collection date | 2003-11-15 |
Detector | CUSTOM-MADE |
Wavelength(s) | 0.97904 |
Spacegroup name | P 43 |
Unit cell lengths | 63.479, 63.479, 112.235 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 35.000 * - 2.200 |
R-factor | 0.212 |
Rwork | 0.212 |
R-free | 0.25300 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | unpublished TruD model SAD data on selenomethionine labeled protein |
RMSD bond length | 0.005 |
RMSD bond angle | 22.400 * |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | CNS |
Refinement software | CNS (1.1) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 40.000 | 2.280 |
High resolution limit [Å] | 2.200 | 2.200 |
Rmerge | 0.039 | 0.215 |
Total number of observations | 88054 * | |
Number of reflections | 22262 | |
<I/σ(I)> | 30.3 | 5.1 |
Completeness [%] | 98.8 | 96.9 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 * | 298 | MES, PEG 8000, ethylene glycol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
1 | VAPOR DIFFUSION, HANGING DROP | 8 * | 298 | MES, PEG 8000, ethylene glycol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
Crystallization Reagents in Literatures
ID | crystal ID | solution | reagent name | concentration (unit) | details |
1 | 1 | drop | protein | 5-10 (mg/ml) | |
2 | 1 | drop | HEPES | 20 (mM) | pH8.0 |
3 | 1 | drop | 250 (mM) | ||
4 | 1 | drop | EDTA | 2 (mM) | |
5 | 1 | drop | dithiothreitol | 2 (mM) | |
6 | 1 | drop | ethylene gylcol | 25 (%(v/v)) | |
7 | 1 | reservoir | MES | 0.1 (M) | pH6.0 |
8 | 1 | reservoir | PEG8000 | 12-14 (%(w/v)) | |
9 | 1 | reservoir | ethylene glycol | 25 (%(v/v)) |