8TKB
tRNA 2-phosphotransferase (Tpt1) from Pyrococcus horikoshii in complex with 5'-AMP
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 | 2023-03-03 |
Detector | DECTRIS EIGER2 X 16M |
Wavelength(s) | 0.9792 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 38.937, 43.665, 122.861 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 41.140 - 1.710 |
R-factor | 0.1859 |
Rwork | 0.185 |
R-free | 0.20920 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 8tfi |
RMSD bond length | 0.012 |
RMSD bond angle | 1.219 |
Data reduction software | XDS |
Data scaling software | XDS |
Phasing software | PHENIX |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 43.670 | 1.740 |
High resolution limit [Å] | 1.710 | 1.710 |
Rmerge | 0.054 | 1.114 |
Rpim | 0.016 | 0.343 |
Number of reflections | 23319 | 1195 |
<I/σ(I)> | 23.5 | 2.1 |
Completeness [%] | 99.4 | 99.5 |
Redundancy | 11.5 | 11.3 |
CC(1/2) | 1.000 | 0.837 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 295 | 0.1 M Tris-Bicine (pH 8.3), 0.1 M amino acid additives mixture (0.02 M each of DL-glutamic acid monohydrate, DL-alanine, glycine, DL-lysine monohydrate and DL-serine), 16-29.6% ethylene glycol, and 8-14.8% PEG-8000 |