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 |