6KBP
Crystal structure of human D-amino acid oxidase mutant (P219L) complexed with benzoate
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PHOTON FACTORY BEAMLINE BL-5A |
Synchrotron site | Photon Factory |
Beamline | BL-5A |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-12-02 |
Detector | DECTRIS PILATUS3 S 6M |
Wavelength(s) | 1.000 |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 149.493, 182.783, 51.039 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 48.300 - 2.250 |
R-factor | 0.1917 |
Rwork | 0.189 |
R-free | 0.24850 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 2du8 |
RMSD bond length | 0.009 |
RMSD bond angle | 1.163 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | MOLREP |
Refinement software | PHENIX (1.14_3260) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 48.300 | 2.300 |
High resolution limit [Å] | 2.250 | 2.250 |
Rmerge | 0.061 | 0.920 |
Rmeas | 0.066 | 1.002 |
Rpim | 0.026 | 0.392 |
Number of reflections | 67535 | 4496 |
<I/σ(I)> | 21.3 | 2.2 |
Completeness [%] | 99.9 | 100 |
Redundancy | 6.6 | 6.4 |
CC(1/2) | 1.000 | 0.811 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 288 | 0.2 M ammonium acetate 12.5% (w/v) polyethylene glycol 4000 10% (v/v) glycerol 0.1 M sodium citrate, pH 8.0 |