1YKV
Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 14-BM-D |
| Synchrotron site | APS |
| Beamline | 14-BM-D |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2002-10-03 |
| Detector | ADSC QUANTUM 4 |
| Wavelength(s) | 1.1 |
| Spacegroup name | P 1 21 1 |
| Unit cell lengths | 78.288, 44.039, 79.998 |
| Unit cell angles | 90.00, 106.87, 90.00 |
Refinement procedure
| Resolution | 20.000 - 3.300 |
| R-factor | 0.22971 |
| Rwork | 0.228 |
| R-free | 0.26206 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | The Diels-Alder ribozyme structure from the Diels-Alder ribozyme-product complex pdb entry 1YLS |
| RMSD bond length | 0.016 |
| RMSD bond angle | 1.480 |
| Data reduction software | HKL-2000 |
| Data scaling software | SCALEPACK |
| Phasing software | AMoRE |
| Refinement software | REFMAC (5.1.9999) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 20.000 | 3.420 |
| High resolution limit [Å] | 3.300 | 3.300 |
| Rmerge | 0.092 | 0.162 |
| Number of reflections | 8392 | |
| <I/σ(I)> | 14 | 8 |
| Completeness [%] | 97.7 | 88.9 |
| Redundancy | 4.9 | 4.4 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | PEG400, sodium HEPES, magnesium chloride, ethylacetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | PEG400 | ||
| 2 | 1 | 1 | sodium HEPES | ||
| 3 | 1 | 1 | H2O | ||
| 4 | 1 | 2 | PEG400 | ||
| 5 | 1 | 2 | sodium HEPES | ||
| 6 | 1 | 2 | magnesium chloride | ||
| 7 | 1 | 2 | ethylacetate | ||
| 8 | 1 | 2 | H2O |
