1K3X
Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | NSLS BEAMLINE X25 |
| Synchrotron site | NSLS |
| Beamline | X25 |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Collection date | 2001-05-29 |
| Detector | BRANDEIS - B4 |
| Spacegroup name | P 43 2 2 |
| Unit cell lengths | 76.495, 76.495, 164.310 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 40.000 * - 1.250 |
| Rwork | 0.149 |
| R-free | 0.18210 * |
| Structure solution method | AB INITIO PHASING |
| Starting model (for MR) | 1k3w |
| RMSD bond length | 0.015 * |
| RMSD bond angle | 2.285 * |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | SHELX |
| Refinement software | SHELXL-97 |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 40.000 | 1.270 |
| High resolution limit [Å] | 1.250 | 1.250 |
| Rmerge | 0.060 * | 0.340 * |
| Total number of observations | 920114 * | |
| Number of reflections | 131559 | |
| <I/σ(I)> | 9.7 | |
| Completeness [%] | 97.4 | 91 |
| Redundancy | 7.5 | 7.5 |
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
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | Ammonium-Sulfate | ||
| 2 | 1 | 1 | Sodium-citrate |
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) | ||
| 3 | 1 | drop | 460 (mM) | ||
| 4 | 1 | drop | protein | 1.8-2.0 (mg/ml) | |
| 5 | 1 | reservoir | ammonium sulfate | 1.8 (M) | |
| 6 | 1 | reservoir | sodium acetate | 0.1 (M) | pH4.6-5.0 |
