1K3W
Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | NSLS BEAMLINE X26C |
| Synchrotron site | NSLS |
| Beamline | X26C |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2001-02-26 |
| Detector | ADSC QUANTUM 4 |
| Spacegroup name | P 43 2 2 |
| Unit cell lengths | 76.030, 76.030, 164.933 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 40.000 * - 1.420 |
| Rwork | 0.165 |
| R-free | 0.20260 |
| Starting model (for MR) | initial MODEL OF BR-URACIL-CONTAINING DNA COMPLEXED WITH ENDONUCLEASE VIII AT 2.4A RESOLUTION |
| RMSD bond length | 0.013 * |
| RMSD bond angle | 2.249 * |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | CNS |
| Refinement software | SHELXL-97 |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 40.000 | 1.440 |
| High resolution limit [Å] | 1.420 | 1.420 |
| Rmerge | 0.080 * | 0.375 * |
| Total number of observations | 471081 * | |
| Number of reflections | 86586 | |
| <I/σ(I)> | 8.9 | |
| Completeness [%] | 95.2 | 71.4 |
| Redundancy | 5.5 | 2 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | Vapor diffusion * | 6.5 | 15 * | 1.8M Ammonium-sulfate, 0.1M sodium-citrate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
Crystallization Reagents in Literatures
| ID | crystal ID | solution | reagent name | concentration (unit) | details |
| 1 | 1 | drop | Tris-HCl | 50 (mM) | |
| 2 | 1 | drop | 5 (mM) | ||
| 4 | 1 | drop | 460 (mM) | ||
| 5 | 1 | drop | protein | 1.8-2.0 (mg/ml) | |
| 6 | 1 | reservoir | ammonium sulfate | 1.8 (M) | |
| 7 | 1 | reservoir | sodium acetate | 0.1 (M) | pH4.6-5.0 |
