2OQ4
Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | APS BEAMLINE 5ID-B |
| Synchrotron site | APS |
| Beamline | 5ID-B |
| Temperature [K] | 100 |
| Detector technology | CCD |
| Detector | MAR CCD 165 mm |
| Wavelength(s) | 1.102 |
| Spacegroup name | P 43 21 2 |
| Unit cell lengths | 107.130, 107.130, 164.860 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 16.000 - 2.600 |
| R-factor | 0.374 |
| Rwork | 0.374 |
| R-free | 0.43200 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 2ea0 |
| RMSD bond length | 0.195 |
| RMSD bond angle | 2.500 |
| Data reduction software | d*TREK |
| Data scaling software | d*TREK |
| Phasing software | CNS |
| Refinement software | CNS (1.0) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 16.730 | 2.690 |
| High resolution limit [Å] | 2.600 | 2.600 |
| Rmerge | 0.083 | 0.338 |
| Number of reflections | 30010 | |
| <I/σ(I)> | 13.1 | |
| Completeness [%] | 99.6 | 98.4 |
| Redundancy | 6.4 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 293 | 1.8M ammonium sulfate, 0.1M sodium acetate pH 4.6-5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystallization Reagents
| ID | crystal ID | solution ID | reagent name | concentration | details |
| 1 | 1 | 1 | ammonium sulfate | ||
| 2 | 1 | 1 | sodium acetate | ||
| 3 | 1 | 1 | h2o | ||
| 4 | 1 | 2 | ammonium sulfate | ||
| 5 | 1 | 2 | sodium acetate | ||
| 6 | 1 | 2 | h2o |
