2EA0
Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli in complex with AP-site containing DNA substrate
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 |
Detector | ADSC QUANTUM 4 |
Wavelength(s) | 1.100 |
Spacegroup name | P 43 2 2 |
Unit cell lengths | 76.184, 76.184, 164.540 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 30.000 - 1.400 |
R-factor | 0.1563 |
R-free | 0.20430 |
Structure solution method | throughout |
Starting model (for MR) | 1k3w |
RMSD bond length | 0.014 |
RMSD bond angle | 0.034 |
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] | 30.000 | 1.420 |
High resolution limit [Å] | 1.400 | 1.400 |
Rmerge | 0.064 | |
Number of reflections | 91763 | |
<I/σ(I)> | 11.6 | |
Completeness [%] | 69.8 | |
Redundancy | 7 |
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 |