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 |