6K1D
Crystal structure of EXD2 exonuclease domain soaked in Mn and GMP
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PAL/PLS BEAMLINE 11C |
Synchrotron site | PAL/PLS |
Beamline | 11C |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-03-07 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.97936 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 46.528, 73.931, 132.543 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 49.348 - 3.000 |
R-factor | 0.2153 |
Rwork | 0.212 |
R-free | 0.27710 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6k17 |
RMSD bond length | 0.010 |
RMSD bond angle | 1.369 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | PHENIX |
Refinement software | PHENIX (1.9_1692) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.000 | 3.050 |
High resolution limit [Å] | 3.000 | 3.000 |
Rmerge | 0.145 | 0.480 |
Number of reflections | 9290 | 465 |
<I/σ(I)> | 12.9 | |
Completeness [%] | 95.7 | |
Redundancy | 5.7 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 277 | PEG 8000, 2-(N-morpholino)ethanesulfonic acid, Calcium acetate, Dithiothreitol, Manganese Chloride, Guanosine monophosphate |