3EY3
A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 5ID-B |
| Synchrotron site | APS |
| Beamline | 5ID-B |
| Temperature [K] | 120 |
| Detector technology | CCD |
| Collection date | 2005-04-03 |
| Detector | MARMOSAIC 225 mm CCD |
| Wavelength(s) | 0.9200 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 40.074, 43.218, 88.712 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 6.900 - 1.250 |
| R-factor | 0.147 |
| Rwork | 0.147 |
| R-free | 0.20700 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | Modified DNA duplex alone from PDB 3EY1 (generated by using the rotation matrix -1.0 0.0 0.0; 0.0 1.0 0.0; 0.0 0.0 -1.0) |
| RMSD bond length | 0.013 |
| RMSD bond angle | 0.028 |
| Data reduction software | XDS |
| Data scaling software | XDS |
| Phasing software | MOLREP |
| Refinement software | SHELXL-97 |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 6.900 | 1.330 |
| High resolution limit [Å] | 1.250 | 1.250 |
| Rmerge | 0.053 | 0.380 |
| Number of reflections | 43276 | |
| <I/σ(I)> | 15.1 | 3.92 |
| Completeness [%] | 96.4 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 291 | 5% MPD, 20 mM Na Cacodylate pH 7.0, 6 mM Spermine tetra-HCl, 20 mM LiCl, 40 mM SrCl2., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | MPD | ||
| 2 | 1 | 1 | Cacodylate | ||
| 3 | 1 | 1 | Spermine tetra-HCl | ||
| 4 | 1 | 1 | LiCl | ||
| 5 | 1 | 1 | SrCl2 | ||
| 6 | 1 | 2 | MPD | ||
| 7 | 1 | 2 | Cacodylate | ||
| 8 | 1 | 2 | LiCl | ||
| 9 | 1 | 2 | SrCl2 |
