1KER
The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-D-glucose bound
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | ESRF BEAMLINE BM14 |
| Synchrotron site | ESRF |
| Beamline | BM14 |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2001-06-06 |
| Detector | ADSC QUANTUM 4 |
| Wavelength(s) | 0.933 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 61.225, 96.151, 182.888 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 49.700 - 2.200 |
| R-factor | 0.175 * |
| Rwork | 0.175 |
| R-free | 0.20600 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | PDB 1G1A |
| RMSD bond length | 0.005 |
| RMSD bond angle | 22.152 * |
| Data reduction software | MOSFLM |
| Data scaling software | CCP4 ((SCALA)) |
| Phasing software | AMoRE |
| Refinement software | CNS (1.0) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 49.700 | 2.320 |
| High resolution limit [Å] | 2.200 | 2.200 |
| Rmerge | 0.112 * | 0.284 * |
| Total number of observations | 179806 * | |
| Number of reflections | 55517 | 8000 * |
| <I/σ(I)> | 5.7 | 2.6 |
| Completeness [%] | 99.8 | 99.9 |
| Redundancy | 3.2 | 3.3 |
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-D-glucose | 15 (mM) | |
| 5 | 1 | drop | thymidine 5'-diphosphate | 15 (mM) | |
| 6 | 1 | reservoir | PEG8000 | 30 (%(w/v)) | |
| 7 | 1 | reservoir | ammonium sulfate | 0.2 (M) | |
| 8 | 1 | reservoir | sodium cacodylate | 0.1 (M) | pH5.4 |
