8GM7
Structure of apurinic/apyrimidinic DNA Lyase TK0353 from Thermococcus kodakarensis (Native 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) | 1.033 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 62.212, 89.925, 130.922 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 47.650 - 1.750 |
R-factor | 0.1908 |
Rwork | 0.188 |
R-free | 0.22020 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.012 |
RMSD bond angle | 1.208 |
Data reduction software | PROTEUM PLUS (3) |
Data scaling software | PROTEUM PLUS (3) |
Phasing software | PHASER |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 48.000 | 1.810 |
High resolution limit [Å] | 1.750 | 1.750 |
Rmerge | 0.109 | 2.035 |
Rmeas | 0.121 | 2.268 |
Rpim | 0.051 | 0.987 |
Number of reflections | 139905 | 13696 |
<I/σ(I)> | 6.6 | 0.9 |
Completeness [%] | 99.2 | 92.6 |
Redundancy | 5.4 | 5.2 |
CC(1/2) | 0.994 | 0.541 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 297 | 2.5 M (NH4)2SO4, cryoprotection by addition of 1.5M Li2SO4 |