8DCB
RNA ligase RtcB from Pyrococcus horikoshii in complex with Ni2+ 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) | 1.4857 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 81.241, 137.492, 149.559 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 49.520 - 2.600 |
R-factor | 0.1723 |
Rwork | 0.170 |
R-free | 0.20860 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4isz |
RMSD bond length | 0.008 |
RMSD bond angle | 0.969 |
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] | 49.850 | 2.680 |
High resolution limit [Å] | 2.600 | 2.600 |
Rpim | 0.047 | 0.326 |
Number of reflections | 52086 | 4421 |
<I/σ(I)> | 15.9 | 2.1 |
Completeness [%] | 99.6 | 99.2 |
Redundancy | 12.9 | 13.9 |
CC(1/2) | 0.998 | 0.762 |
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 NiCl2, 10 mM GTP soak duration: 60 min cryoprotectant: 2.0 M ammonium sulfate, 0.2 M lithium sulfate, 5 mM NiCl2, 5 mM GTP, 20 %(w/v) sucrose |