8DL3
Crystal structure of the human queuine salvage enzyme DUF2419, complexed with queuine
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRL BEAMLINE BL12-2 |
Synchrotron site | SSRL |
Beamline | BL12-2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2022-06-25 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.97946 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 42.726, 136.759, 52.606 |
Unit cell angles | 90.00, 90.33, 90.00 |
Refinement procedure
Resolution | 42.760 - 2.260 |
R-factor | 0.1587 |
Rwork | 0.156 |
R-free | 0.22210 |
Structure solution method | FOURIER SYNTHESIS |
Starting model (for MR) | 7ugk |
RMSD bond length | 0.007 |
RMSD bond angle | 1.205 |
Data reduction software | HKL-3000 (v721.3) |
Data scaling software | HKL-3000 (v721.3) |
Refinement software | REFMAC (5.8.0222) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 45.000 | 45.000 | 2.290 |
High resolution limit [Å] | 2.250 | 6.100 | 2.250 |
Rmerge | 0.226 | 0.077 | 1.516 |
Rmeas | 0.245 | 0.084 | 1.678 |
Rpim | 0.095 | 0.032 | 0.705 |
Total number of observations | 180879 | ||
Number of reflections | 27661 | 1419 | 1304 |
<I/σ(I)> | 4.1 | ||
Completeness [%] | 97.9 | 98.3 | 94.5 |
Redundancy | 6.5 | 6.9 | 5.2 |
CC(1/2) | 0.996 | 0.478 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | 0.2M NaCl, 25% PEG3350, 0.1M Bis-Tris, pH 5.5 |