2FIJ
Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-aU-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and Arabino-Uridine (aU)
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 5ID-B |
| Synchrotron site | APS |
| Beamline | 5ID-B |
| Temperature [K] | 103 |
| Detector technology | CCD |
| Collection date | 2003-06-21 |
| Detector | MARRESEARCH |
| Wavelength(s) | 1.60914 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 32.277, 32.469, 66.749 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 33.370 - 1.190 |
| R-factor | 0.15856 |
| Rwork | 0.157 |
| R-free | 0.16922 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | NDB entry AD0007/PDB entry 1DPL |
| RMSD bond length | 0.007 |
| RMSD bond angle | 1.260 |
| Data scaling software | XDS |
| Phasing software | EPMR |
| Refinement software | REFMAC (5.2.0005) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 33.370 | 1.270 |
| High resolution limit [Å] | 1.190 | 1.190 |
| Rmerge | 0.063 | 0.290 |
| Number of reflections | 21724 | |
| <I/σ(I)> | 13.4 | 3.7 |
| Completeness [%] | 93.7 | 91 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.5 | 291 | Final droplet composition: 1 mM oligonucleotide, 10% MPD, 20 mM sodium cacodylate, pH 5.5, 10 mM cobalt hexamine, 20 mM LiCl and 10 mM MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | MPD | ||
| 10 | 1 | 2 | LiCl | ||
| 11 | 1 | 2 | MgCl2 | ||
| 12 | 1 | 2 | H2O | ||
| 2 | 1 | 1 | sodium cacodylate | ||
| 3 | 1 | 1 | cobalt hexamine | ||
| 4 | 1 | 1 | LiCl | ||
| 5 | 1 | 1 | MgCl2 | ||
| 6 | 1 | 1 | H2O | ||
| 7 | 1 | 2 | MPD | ||
| 8 | 1 | 2 | sodium cacodylate | ||
| 9 | 1 | 2 | cobalt hexamine |
