5EZF
Racemic crystal structures of Pribnow box consensus promoter sequence (Pbca)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SOLEIL BEAMLINE PROXIMA 1 |
Synchrotron site | SOLEIL |
Beamline | PROXIMA 1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2015-06-11 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.9785 |
Spacegroup name | P b c a |
Unit cell lengths | 41.736, 39.329, 65.713 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 32.856 - 1.650 |
R-factor | 0.2973 |
Rwork | 0.296 |
R-free | 0.31670 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1fq2 |
RMSD bond length | 0.007 |
RMSD bond angle | 1.626 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHASER |
Refinement software | PHENIX (1.8.2_1309) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 32.860 | 1.790 |
High resolution limit [Å] | 1.650 | 1.650 |
Rmerge | 0.019 | 0.268 |
Number of reflections | 12549 | |
<I/σ(I)> | 16.92 | 2.75 |
Completeness [%] | 99.9 | 99.76 |
Redundancy | 1.9 | 1.9 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | Racemic DNA mixture*, HEPES, calcium chloride, PEG400 * For crystallization, we used four strands 1) d(CGCTATAATGCG) with L-sugars 2) d(CGCATTATAGCG) with L-sugars and 3) d(CGCTATAATGCG) with D-sugars 4) d(CGCATTATAGCG) with D-sugars Enantio-pure DNA solutions were prepared first by de-naturation followed by slow cooling down process to ensure proper folding of the hetero-duplex formed between the non-self complementary strands. After slow-annealing, the enantiopure solutions were mixed in equimolar ratio and this racemic DNA mixture was used for crystallization. |