3D2X
Structure of the thiamine pyrophosphate-specific riboswitch bound to oxythiamine pyrophosphate
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 | 2006-08-11 |
Detector | MARMOSAIC 225 mm CCD |
Wavelength(s) | 1.0 |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 75.497, 111.172, 55.375 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 15.000 - 2.500 |
R-factor | 0.254 |
Rwork | 0.233 |
R-free | 0.26700 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2cky |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHASER |
Refinement software | CNS (1.1) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 15.000 | 2.550 |
High resolution limit [Å] | 2.500 | 2.500 |
Rmerge | 0.153 | 0.533 |
Number of reflections | 16268 | |
<I/σ(I)> | 14.6 | 2.85 |
Completeness [%] | 97.2 | 97.1 |
Redundancy | 7.3 | 7.5 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.8 | 298 | 12-18% 1,6-hexanediol, 0.5mM spermine, 10mM magnesium sulfate, 40mM sodium cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystallization Reagents
ID | crystal ID | solution ID | reagent name | concentration | details |
1 | 1 | 1 | 1,6-hexanediol | ||
2 | 1 | 2 | 1,6-hexanediol | ||
3 | 1 | 1 | spermine | ||
4 | 1 | 1 | magnesium sulfate | ||
5 | 1 | 2 | magnesium sulfate | ||
6 | 1 | 1 | sodium cacodylate | ||
7 | 1 | 2 | sodium cacodylate |