6BLJ
Crystal structure of cytoplasmic Serine-tRNA ligase from Naegleria fowleri in complex with AMP
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 21-ID-G |
Synchrotron site | APS |
Beamline | 21-ID-G |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2016-07-14 |
Detector | RAYONIX MX-300 |
Wavelength(s) | 0.97856 |
Spacegroup name | P 31 2 1 |
Unit cell lengths | 168.190, 168.190, 111.500 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 42.047 - 2.100 |
R-factor | 0.1588 |
Rwork | 0.158 |
R-free | 0.19110 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 3lsq via Morda |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | MoRDa (3.22) |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 42.047 | 42.047 | 2.150 |
High resolution limit [Å] | 2.100 | 9.390 | 2.100 |
Rmerge | 0.071 | 0.028 | 0.544 |
Rmeas | 0.077 | 0.030 | 0.584 |
Number of reflections | 105635 | 1246 | 7738 |
<I/σ(I)> | 18.67 | 40.93 | 4.31 |
Completeness [%] | 99.8 | 95.8 | 100 |
Redundancy | 7.457 | 6.677 | 7.561 |
CC(1/2) | 0.999 | 0.998 | 0.897 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | Microlytic MCSG1 screen, B8:25.5% PEG 4000, 15% glycerol, 170mM NaOAc: NafoA.01238.a.B1.PW37973 at 32.5mg/ml + 3mM L-Serine + 3mM AMPPNP + 3mM MgCl2: cryo: direct: tray 286789b8, puck PEM7-1 |