3PD4
Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with glycyl-3'-aminoadenosine
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU RUH3R |
Temperature [K] | 100 |
Detector technology | IMAGE PLATE |
Collection date | 2009-05-17 |
Detector | MAR scanner 345 mm plate |
Wavelength(s) | 1.5418 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 40.335, 69.083, 94.659 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 24.850 - 2.400 |
R-factor | 0.2076 |
Rwork | 0.204 |
R-free | 0.28924 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1y2q |
RMSD bond length | 0.014 |
RMSD bond angle | 1.594 |
Data reduction software | DENZO |
Data scaling software | SCALEPACK |
Phasing software | MOLREP |
Refinement software | CNS (1.1) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 25.000 | 2.490 |
High resolution limit [Å] | 2.400 | 2.400 |
Rmerge | 0.109 | 0.291 |
Number of reflections | 10812 | |
<I/σ(I)> | 15.2 | 3.5 |
Completeness [%] | 98.7 | 87.6 |
Redundancy | 4.6 | 3.9 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 298 | PEG 3350, Bis-Tris, NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |