8B02
Crystal structure of the dsRBD domain of tRNA-dihydrouridine(20) synthase from Amphimedon queenslandica
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SOLEIL BEAMLINE PROXIMA 2 |
Synchrotron site | SOLEIL |
Beamline | PROXIMA 2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-11-16 |
Detector | DECTRIS EIGER X 9M |
Wavelength(s) | 0.98011 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 29.077, 56.895, 63.587 |
Unit cell angles | 90.00, 93.05, 90.00 |
Refinement procedure
Resolution | 29.040 - 1.676 |
R-factor | 0.2047 |
Rwork | 0.203 |
R-free | 0.22780 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4wft |
RMSD bond length | 0.009 |
RMSD bond angle | 1.020 |
Data reduction software | autoPROC (1.0.5) |
Data scaling software | XDS (Jan 10, 2022 (BUILT 20220220)) |
Phasing software | PHASER (2.8.2) |
Refinement software | BUSTER (2.10.4 (8-JUN-2022)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 42.373 | 1.705 |
High resolution limit [Å] | 1.676 | 1.676 |
Rmerge | 0.074 | 0.975 |
Rmeas | 0.090 | 1.245 |
Rpim | 0.051 | 0.762 |
Number of reflections | 23361 | 963 |
<I/σ(I)> | 7.8 | 0.8 |
Completeness [%] | 97.9 | 79.7 |
Redundancy | 2.9 | 2 |
CC(1/2) | 0.997 | 0.351 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 292 | 0.1 M Hepes pH 7.5, 1.4 M tri-sodium citrate, 15 mg/ml protein in 50 mM Tris, pH 8 300 mM NaCl 5mM mercaptoethanol |