8SYJ
Structure of apurinic/apyrimidinic DNA lyase TK0353 from Thermococcus kodakarensis (Iodide crystal form)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 23-ID-D |
Synchrotron site | APS |
Beamline | 23-ID-D |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-10-20 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 1.28 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 63.554, 89.116, 128.043 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 38.490 - 2.200 |
R-factor | 0.2288 |
Rwork | 0.225 |
R-free | 0.26000 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.006 |
RMSD bond angle | 0.904 |
Data reduction software | DIALS (2.2.5) |
Data scaling software | DIALS (2.2.5) |
Phasing software | PHASER |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 40.000 | 2.270 |
High resolution limit [Å] | 2.200 | 2.200 |
Rmerge | 0.127 | 1.270 |
Rpim | 0.051 | 0.561 |
Number of reflections | 70908 | 6310 |
<I/σ(I)> | 8.2 | 1.6 |
Completeness [%] | 99.8 | |
Redundancy | 6.1 | |
CC(1/2) | 0.997 | 0.809 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 297 | 2.5 M ammonium sulfate cryoprotected by inclusion of 1.5 M lithium sulfate and soaked in the presence of 0.1 M sodium iodide |