1KEP
The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-xylose bound
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | SRS BEAMLINE PX9.6 |
| Synchrotron site | SRS |
| Beamline | PX9.6 |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2001-06-04 |
| Detector | ADSC QUANTUM 4 |
| Wavelength(s) | 0.870 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 62.449, 97.182, 185.471 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 91.300 * - 1.800 |
| R-factor | 0.145 * |
| Rwork | 0.145 |
| R-free | 0.17238 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | PDB 1G1A |
| RMSD bond length | 0.007 * |
| RMSD bond angle | 1.280 * |
| Data reduction software | MOSFLM |
| Data scaling software | CCP4 ((SCALA)) |
| Phasing software | AMoRE |
| Refinement software | REFMAC (5.0) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 91.300 | 1.900 |
| High resolution limit [Å] | 1.800 | 1.800 |
| Rmerge | 0.079 * | 0.291 * |
| Total number of observations | 340418 * | |
| Number of reflections | 102080 * | 12822 * |
| <I/σ(I)> | 6.9 | 2.5 |
| Completeness [%] | 97.0 | 85.1 |
| Redundancy | 3.3 | 2.3 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | Vapor diffusion, sitting drop * | 5.4 | 293 | used microseeding * |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | protein | 3.6 (mg/ml) | |
| 2 | 1 | drop | dithiothreitol | 2.5 (mM) | |
| 3 | 1 | drop | NAD+ | 4 (mM) | |
| 4 | 1 | drop | dTDP-xylose | 7 (mM) | |
| 5 | 1 | reservoir | PEG4000 | 35 (%(w/v)) | |
| 6 | 1 | reservoir | citric acid | 0.1 (M) | pH5.4 |
| 7 | 1 | reservoir | ammonium sulfate | 0.3 (M) |
