2QS6
Structure of a Hoogsteen antiparallel duplex with extra-helical thymines
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE BM16 |
Synchrotron site | ESRF |
Beamline | BM16 |
Temperature [K] | 113.15 |
Detector technology | CCD |
Collection date | 2004-03-06 |
Detector | MAR CCD 165 mm |
Wavelength(s) | 0.9790 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 120.836, 39.540, 71.753 |
Unit cell angles | 90.00, 95.08, 90.00 |
Refinement procedure
Resolution | 71.430 - 3.080 |
R-factor | 0.21446 |
Rwork | 0.207 |
R-free | 0.28950 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | D(ATATAT)2 model with Hoogsteen base pairs (from NDB entry UD0049) |
RMSD bond length | 0.085 |
RMSD bond angle | 1.070 |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | AMoRE |
Refinement software | REFMAC (5.3.0034) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 71.430 | 3.210 |
High resolution limit [Å] | 3.080 | 3.080 |
Rmerge | 0.077 | 0.222 |
Number of reflections | 6262 | |
<I/σ(I)> | 13.5 | 3.6 |
Completeness [%] | 98.0 | 94.2 |
Redundancy | 5.35 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | Drop: 1.0mM octamer, 10% MPD, 22mM sodium cacodylate, 10mM magnesium chloride, 1.5mM spermine tetrachloride. Reservoir: from 25% to 45% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystallization Reagents
ID | crystal ID | solution ID | reagent name | concentration | details |
1 | 1 | 1 | 0% MPD | ||
2 | 1 | 1 | sodium cacodylate | ||
3 | 1 | 1 | magnesium chloride | ||
4 | 1 | 1 | spermine tetrachloride | ||
5 | 1 | 2 | 25% to 45% MPD |