2FIL
Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-faT-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and 2'-Fluoroarabino-Thymidine (faT)
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) | 1.0 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 32.733, 69.180, 32.831 |
Unit cell angles | 90.00, 92.21, 90.00 |
Refinement procedure
Resolution | 30.000 - 1.690 |
R-factor | 0.20401 |
Rwork | 0.203 |
R-free | 0.21543 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | NDB entry AD0007/PDB entry 1DPL |
RMSD bond length | 0.015 |
RMSD bond angle | 2.590 |
Data scaling software | XDS |
Phasing software | EPMR |
Refinement software | REFMAC (5.2.0005) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 30.000 | 1.800 |
High resolution limit [Å] | 1.690 | 1.690 |
Rmerge | 0.094 | 0.347 |
Number of reflections | 15695 | |
<I/σ(I)> | 8.1 | 2.8 |
Completeness [%] | 95.4 | 95.8 |
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, 6 mM NaCl and 80 mM KCl., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystallization Reagents
ID | crystal ID | solution ID | reagent name | concentration | details |
1 | 1 | 1 | MPD | ||
10 | 1 | 2 | NaCl | ||
11 | 1 | 2 | KCl | ||
12 | 1 | 2 | H2O | ||
2 | 1 | 1 | sodium cacodylate | ||
3 | 1 | 1 | cobalt hexamine | ||
4 | 1 | 1 | NaCl | ||
5 | 1 | 1 | KCl | ||
6 | 1 | 1 | H2O | ||
7 | 1 | 2 | MPD | ||
8 | 1 | 2 | sodium cacodylate | ||
9 | 1 | 2 | cobalt hexamine |