2OPF
Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (R252A) 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 |
| Collection date | 2001-12-24 |
| Detector | MAR CCD 165 mm |
| Wavelength(s) | 1.102 |
| Spacegroup name | P 43 2 2 |
| Unit cell lengths | 73.556, 73.556, 170.113 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 20.410 - 1.850 |
| R-factor | 0.24 |
| Rwork | 0.240 |
| R-free | 0.26700 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 2ea0 |
| RMSD bond length | 0.005 |
| RMSD bond angle | 1.200 |
| Data reduction software | DENZO |
| Data scaling software | SCALEPACK |
| Phasing software | CNS |
| Refinement software | CNS (1.0) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 40.000 | 1.880 |
| High resolution limit [Å] | 1.850 | 1.850 |
| Rmerge | 0.099 | 0.491 |
| Number of reflections | 39078 | |
| <I/σ(I)> | 7.4 | |
| Completeness [%] | 98.9 | 96 |
| Redundancy | 13 |
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 |
