1YKQ
Crystal structure of Diels-Alder ribozyme
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | NSLS BEAMLINE X25 |
| Synchrotron site | NSLS |
| Beamline | X25 |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2004-06-13 |
| Detector | ADSC QUANTUM 315 |
| Wavelength(s) | 1.1 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 77.690, 44.240, 79.640 |
| Unit cell angles | 90.00, 107.12, 90.00 |
Refinement procedure
| Resolution | 20.000 - 3.500 |
| R-factor | 0.2875 |
| Rwork | 0.286 |
| R-free | 0.32380 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | Diels-Alder ribozyme from the ribozyme-product complex pdb entry 1YLS |
| RMSD bond length | 0.015 |
| RMSD bond angle | 1.612 |
| Data reduction software | HKL-2000 |
| Data scaling software | SCALEPACK |
| Phasing software | SHARP |
| Refinement software | REFMAC (5.1.9999) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 20.000 | 3.620 |
| High resolution limit [Å] | 3.500 | 3.500 |
| Rmerge | 0.154 | 0.729 |
| Number of reflections | 6744 | |
| <I/σ(I)> | 8.1 | 1.8 |
| Completeness [%] | 97.7 | 98.2 |
| Redundancy | 3.8 | 3.8 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | PEG400, sodium cacodylate, magnesium acetate, 1,6-hexandiol, sodium chloride, cadmium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | PEG400 | ||
| 10 | 1 | 2 | H2O | ||
| 2 | 1 | 1 | sodium cacodylate | ||
| 3 | 1 | 1 | H2O | ||
| 4 | 1 | 2 | PEG400 | ||
| 5 | 1 | 2 | sodium cacodylate | ||
| 6 | 1 | 2 | magnesium acetate | ||
| 7 | 1 | 2 | 1,6-hexandiol | ||
| 8 | 1 | 2 | sodium chloride | ||
| 9 | 1 | 2 | cadmium chloride |
