6NAB
Crystal structure of prolyl-tRNA synthetase from Naegleria fowleri in complex with proline and adenosine monophophsphate (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 | 2018-07-14 |
Detector | RAYONIX MX-300 |
Wavelength(s) | 0.97856 |
Spacegroup name | C 1 2 1 |
Unit cell lengths | 156.930, 66.100, 112.980 |
Unit cell angles | 90.00, 102.03, 90.00 |
Refinement procedure
Resolution | 38.372 - 2.000 |
R-factor | 0.1522 |
Rwork | 0.151 |
R-free | 0.19160 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 4hvcAB as per MoRDa |
RMSD bond length | 0.007 |
RMSD bond angle | 0.843 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | SIMBAD |
Refinement software | PHENIX ((dev_3339)) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 38.372 | 38.372 | 2.050 |
High resolution limit [Å] | 2.000 | 8.940 | 2.000 |
Rmerge | 0.080 | 0.031 | 0.495 |
Rmeas | 0.094 | 0.036 | 0.606 |
Total number of observations | 279947 | ||
Number of reflections | 76263 | 900 | 5333 |
<I/σ(I)> | 12.78 | 35.68 | 2.24 |
Completeness [%] | 99.4 | 96.6 | 94.4 |
Redundancy | 3.671 | 3.39 | 2.823 |
CC(1/2) | 0.997 | 0.998 | 0.739 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | Anatrace TOP86 screen, condition D7: 200mM Ammonium sulfate, 30% PEG 8000: NAFOA.18681.a.B2.PW37988 at 22.6mg/ml + 5mM CaCl2: cryo 15% EG: tray 287001 d7: puck XFD3-8 |