7OT3
Human Prolyl-tRNA Synthetase in Complex with L-proline and Compound 3b
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SLS BEAMLINE X06SA |
Synchrotron site | SLS |
Beamline | X06SA |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-04-22 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 1.000021 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 71.871, 92.422, 87.260 |
Unit cell angles | 90.00, 108.88, 90.00 |
Refinement procedure
Resolution | 54.770 - 2.530 |
R-factor | 0.2208 |
Rwork | 0.218 |
R-free | 0.27610 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5vad |
Data reduction software | XDS |
Data scaling software | Aimless (0.7.4) |
Phasing software | PHASER |
Refinement software | PHENIX (1.17.1_3660) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 54.770 | 54.770 | 2.610 |
High resolution limit [Å] | 2.480 | 7.840 | 2.480 |
Rmerge | 0.047 | 0.029 | 0.985 |
Rmeas | 0.051 | 0.032 | 1.064 |
Rpim | 0.019 | 0.012 | 0.398 |
Total number of observations | 264382 | 8573 | 38617 |
Number of reflections | 38157 | 1267 | 5511 |
<I/σ(I)> | 17.1 | 46.4 | 1.7 |
Completeness [%] | 99.2 | 99.7 | 99.2 |
Redundancy | 6.9 | 6.8 | 7 |
CC(1/2) | 0.999 | 0.999 | 0.749 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | MICROBATCH | 7.5 | 293 | The purified protein at 30 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was incubated with 10 mM L-proline, 2 mM compound and 12% (v/v) DMSO on ice for 1 hr. Crystals were grown in a Terasaki Microbatch plate by mixing 1 uL the pre-mix with 1 uL of reservoir solution containing 0.25-0.4 M SrCl2, 15-20% (v/v) PEG3350 and 100 mM HEPES pH 7.5. The drops were covered with paraffin oil. Crystals were flash frozen in liquid nitrogen directly from the plate. |