6UYH
Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with halofuginone and AMPPNP
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-F |
Synchrotron site | APS |
Beamline | 21-ID-F |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2019-10-23 |
Detector | RAYONIX MX-300 |
Wavelength(s) | 0.9785 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 157.290, 66.540, 112.560 |
Unit cell angles | 90.00, 101.74, 90.00 |
Refinement procedure
Resolution | 42.660 - 1.750 |
R-factor | 0.155 |
Rwork | 0.154 |
R-free | 0.18000 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 6nab |
RMSD bond length | 0.006 |
RMSD bond angle | 0.826 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | PHASER |
Refinement software | PHENIX (1.17RC1_3602) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 50.000 | 1.800 |
High resolution limit [Å] | 1.750 | 7.830 | 1.750 |
Rmerge | 0.052 | 0.023 | 0.517 |
Rmeas | 0.060 | 0.027 | 0.592 |
Number of reflections | 114792 | 1356 | 8431 |
<I/σ(I)> | 15.69 | 38.5 | 2.52 |
Completeness [%] | 99.9 | 98.3 | 99.9 |
Redundancy | 4.173 | 3.902 | 4.203 |
CC(1/2) | 0.999 | 0.999 | 0.813 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | NafoA.18681.a.B2.PW37988 at 34 mg/ml, incubated with 2 mM MgCl2, AMPPNP, halofuginone, mixed 1:1 with MCSG1(a6): 25% (w/v) PEG-3350, 0.1 M Bis-Tris/HCl, pH = 5.5, 0.2 M ammonium sulfate, cryoprotected with ethlyene glycol. Barcode: 310518a6, puck: xux0-7. |