5TRW
Crystal structure of Pyridoxamine kinase PDXY from Burkholderia xenovorans
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 | 2016-10-06 |
Detector | RAYONIX MX-300 |
Wavelength(s) | 0.97872 |
Spacegroup name | P 41 21 2 |
Unit cell lengths | 58.870, 58.870, 175.770 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 43.942 - 1.600 |
R-factor | 0.1524 |
Rwork | 0.151 |
R-free | 0.17920 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1vi9 |
RMSD bond length | 0.008 |
RMSD bond angle | 0.933 |
Data reduction software | XDS |
Data scaling software | XSCALE |
Phasing software | MOLREP |
Refinement software | PHENIX |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 50.000 | 1.640 | |
High resolution limit [Å] | 1.600 | 7.160 | 1.600 |
Rmerge | 0.075 | 0.038 | 0.559 |
Number of reflections | 41948 | ||
<I/σ(I)> | 18.7 | 37.95 | 3.98 |
Completeness [%] | 100.0 | 98.5 | 100 |
Redundancy | 9.51 | ||
CC(1/2) | 0.999 | 0.998 | 0.912 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 290 | Microlytic MCSG1 screen H7: 30% PEG 3000, 100mM CHES pH 9.5; BuxeA.00129.a.B1.PS37942 at 14.1mg/ml + 3mM MgCl2 + 3mM AMPPNP (not visible); cryo: 20% EG; tray 274724a2, puck JUS9-5 |