6YKT
Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Compound 11e
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SOLEIL BEAMLINE PROXIMA 1 |
Synchrotron site | SOLEIL |
Beamline | PROXIMA 1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-02-15 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.978566 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 49.235, 80.987, 224.117 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 65.639 - 2.320 |
R-factor | 0.1862 |
Rwork | 0.184 |
R-free | 0.23700 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6q89 |
Data reduction software | XDS |
Data scaling software | Aimless (0.7.4) |
Phasing software | PHASER |
Refinement software | PHENIX (1.15.2_3472) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 112.060 | 112.060 | 2.320 |
High resolution limit [Å] | 2.200 | 6.960 | 2.200 |
Rmerge | 0.110 | 0.046 | 1.187 |
Rmeas | 0.117 | 0.050 | 1.265 |
Rpim | 0.040 | 0.017 | 0.430 |
Total number of observations | 383999 | 12325 | 55233 |
Number of reflections | 46442 | 1659 | 6662 |
<I/σ(I)> | 11.2 | 32.6 | 1.7 |
Completeness [%] | 99.9 | 99.8 | 99.7 |
Redundancy | 8.3 | 7.4 | 8.3 |
CC(1/2) | 0.998 | 0.998 | 0.684 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was mixed with 0.1 M bis-tris propane pH 8.5, 0.1 M MgCl2, 20% w/v PEG 3350 and a crystal seed stock in a 0.75:1.0:0.25 (v/v) ratio. The seed stock was prepared in the same crystallization buffer. Suitable crystals were soaked with 2 mM synthesized compound 11e in an equilvalent precipitant solution supplemented with 22% v/v ethylene glycol. |