1RK2
E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP, SOLVED IN SPACE GROUP P212121
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | EMBL/DESY, HAMBURG BEAMLINE X11 |
Synchrotron site | EMBL/DESY, HAMBURG |
Beamline | X11 |
Temperature [K] | 100 |
Detector technology | IMAGE PLATE |
Collection date | 1998-05 |
Detector | MARRESEARCH |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 55.201, 62.492, 337.800 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 13.000 - 2.250 |
Rwork | 0.228 |
R-free | 0.26500 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1RKD: RESIDUES 4-9 44-93 123-241 AND 254-309 |
RMSD bond length | 0.007 |
RMSD bond angle | 1.440 * |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | AMoRE |
Refinement software | CNS (0.5) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 13.000 | 2.290 |
High resolution limit [Å] | 2.250 | 2.250 |
Rmerge | 0.072 | 0.291 |
Total number of observations | 188129 * | |
Number of reflections | 55979 | |
<I/σ(I)> | 17 | 3.9 |
Completeness [%] | 99.1 | 98.8 |
Redundancy | 4 | 4 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | Vapor diffusion, hanging drop * | 4.8 | 20 * | CRYSTALS WERE GROWN IN THE PRESENCE OF 5 MM RIBOSE, 10 MM ADP, 0.05 MM ALF4 AND 15 MM NAF USING 8.8-15% PEG 4000, 0.25 M MGCL2 AND 20% MPD IN 0.1 M TRIS- HCL BUFFERED TO PH 4.8. |
Crystallization Reagents in Literatures
ID | crystal ID | solution | reagent name | concentration (unit) | details |
1 | 1 | drop | ribokinase | 3-3.5 (mg/ml) | |
2 | 1 | reservoir | ribose | 5 (mM) | |
3 | 1 | reservoir | ADP | 10 (mM) | |
4 | 1 | reservoir | AIF3 | 0.05 (mM) | |
5 | 1 | reservoir | 15 (mM) | ||
6 | 1 | reservoir | sodium acetate | 0.1 (M) | |
7 | 1 | reservoir | 0.25 (M) | ||
8 | 1 | reservoir | MPD | 20 (%(v/v)) | |
9 | 1 | reservoir | PEG4000 | 8.8-15 (%(w/v)) |