7AP4
Thermus thermophilus Aspartyl-tRNA Synthetase in Complex with Compound AspS7HMDDA
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | ESRF BEAMLINE ID29 |
Synchrotron site | ESRF |
Beamline | ID29 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-02-16 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 0.96863 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 82.277, 112.531, 88.253 |
Unit cell angles | 90.00, 104.86, 90.00 |
Refinement procedure
Resolution | 79.526 - 2.150 |
R-factor | 0.1995 |
Rwork | 0.199 |
R-free | 0.24050 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1l0w |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX (1.15.2_3472) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 79.530 | 79.530 | 2.170 |
High resolution limit [Å] | 2.060 | 6.510 | 2.060 |
Rmerge | 0.071 | 0.051 | 0.699 |
Rmeas | 0.082 | 0.059 | 0.808 |
Rpim | 0.041 | 0.030 | 0.401 |
Total number of observations | 356281 | 11041 | 53328 |
Number of reflections | 94888 | 3083 | 13811 |
<I/σ(I)> | 9.5 | 21.4 | 1.7 |
Completeness [%] | 99.0 | 98.7 | 98.6 |
Redundancy | 3.8 | 3.6 | 3.9 |
CC(1/2) | 0.997 | 0.996 | 0.741 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION | 7 | 293 | A 10 mg/ml protein solution was prepared in 10 mM TRIS pH 7.5, 100 mM NaCl, 2.5 mM DTT and 0.4% w/v low melting point agarose, maintaining the sample temperature at 315 kelvin. Crystals were grown by mixing an equal volume of the protein solution with 8-12% PEG 4000, 0.1 M Morpheus buffer system 1 (MES/imidazole) pH 7, 100 mM KCl, 20 v/v % glycerol. For soaking a 4 mM solution of compound in DMSO was used. A one third volume of the initial drop size was pipetted carefully onto the crystal containing drop. The sample was then placed back over the reservoir and incubated for approximately 2 hr. Crystals were caught in cryoloops and directly flash frozen in liquid nitrogen. |