8DCA
RNA ligase RtcB from Pyrococcus horikoshii in complex with Co2+ and GTP
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 24-ID-C |
Synchrotron site | APS |
Beamline | 24-ID-C |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-10-31 |
Detector | DECTRIS EIGER2 X 16M |
Wavelength(s) | 1.6060 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 81.161, 138.864, 149.877 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 49.770 - 2.430 |
R-factor | 0.1781 |
Rwork | 0.177 |
R-free | 0.20320 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4isz |
RMSD bond length | 0.008 |
RMSD bond angle | 1.036 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHASER |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 49.960 | 2.490 |
High resolution limit [Å] | 2.430 | 2.430 |
Rpim | 0.047 | 0.337 |
Number of reflections | 64578 | 4462 |
<I/σ(I)> | 22.7 | 2.1 |
Completeness [%] | 100.0 | 100 |
Redundancy | 19.3 | 19.4 |
CC(1/2) | 0.995 | 0.745 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 295 | apoenzyme: 0.12 mM protein, 2.1 M ammonium sulfate, 0.2 M lithium sulfate soak: 2.1 M ammonium sulfate, 0.2 M lithium sulfate, 10 mM CoCl2, 10 mM GTP soak duration: 60 min cryoprotectant: 2.0 M ammonium sulfate, 0.2 M lithium sulfate, 5 mM CoCl2, 5 mM GTP, 20 % (w/v) sucrose |