2OKS
X-ray Structure of a DNA Repair Substrate Containing an Alkyl Interstrand Crosslink at 1.65 Resolution
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU |
Temperature [K] | 200 |
Detector technology | IMAGE PLATE |
Collection date | 2004-08-01 |
Detector | RIGAKU RAXIS IV |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 31.870, 24.890, 34.350 |
Unit cell angles | 90.00, 114.50, 90.00 |
Refinement procedure
Resolution | 18.890 - 1.650 |
Rwork | 0.182 |
R-free | 0.20800 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 1en8 |
RMSD bond length | 0.012 |
RMSD bond angle | 1.100 |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | CNS |
Refinement software | CNS (1.1) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 40.000 | 1.710 |
High resolution limit [Å] | 1.650 | 1.650 |
Number of reflections | 2924 | |
<I/σ(I)> | 38.1 | 25.7 |
Completeness [%] | 96.1 | 79.4 |
Redundancy | 4.1 | 2.56 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | 8 | The purified crosslinked DNA was dissolved in a buffer containing 22 mM ammonium acetate, 11 mM tris-hydroxymethyl-aminomethane (Tris)-HCl pH 8.0, and 11 mM calcium acetate. Crystals were grown using the sitting drop vapor diffusion method at 277K, in which 3 uL of a reservoir solution containing 27% 2-3 methyl-pentadiol, 115 mM calcium acetate, and 10 mM Tris-HCl pH 8.0 was added to an equal volume of DNA solution, and the mixture was equilibrated against 700 uL of the reservoir solution. Crystals first appeared after two weeks. |
Crystallization Reagents
ID | crystal ID | solution ID | reagent name | concentration | details |
1 | 1 | 1 | 2-3 methyl-pentadiol | ||
2 | 1 | 1 | calcium acetate | ||
3 | 1 | 1 | Tris-HCl | ||
4 | 1 | 1 | ammonium acetate | ||
5 | 1 | 1 | H2O | ||
6 | 1 | 2 | 2-3 methyl-pentadiol | ||
7 | 1 | 2 | calcium acetate | ||
8 | 1 | 2 | Tris-HCl | ||
9 | 1 | 2 | H2O |