6H00
Crystal structure of human pyridoxine 5-phophate oxidase, R116Q variant
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | DIAMOND BEAMLINE I02 |
| Synchrotron site | Diamond |
| Beamline | I02 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2016-04-15 |
| Detector | DECTRIS PILATUS 6M-F |
| Wavelength(s) | 0.979 |
| Spacegroup name | P 31 2 1 |
| Unit cell lengths | 83.330, 83.330, 58.930 |
| Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
| Resolution | 34.030 - 1.660 |
| R-factor | 0.1705 |
| Rwork | 0.169 |
| R-free | 0.20330 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 1nrg |
| RMSD bond length | 0.012 |
| RMSD bond angle | 1.538 |
| Data reduction software | xia2 |
| Data scaling software | Aimless (0.5.23) |
| Phasing software | PHASER |
| Refinement software | REFMAC (5.8.0135) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 34.030 | 34.030 | 1.700 |
| High resolution limit [Å] | 1.660 | 7.420 | 1.660 |
| Rmerge | 0.036 | 0.037 | 1.053 |
| Rmeas | 0.042 | 0.043 | 1.207 |
| Rpim | 0.020 | 0.022 | 0.578 |
| Total number of observations | 116657 | 1244 | 8744 |
| Number of reflections | 29800 | 345 | 2087 |
| <I/σ(I)> | 17.9 | 47.9 | 1.4 |
| Completeness [%] | 99.7 | 95.3 | 99.8 |
| Redundancy | 4.1 | 3.6 | 4.2 |
| CC(1/2) | 0.999 | 0.997 | 0.514 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 277.15 | 20% PEG1000, 0.2 M lithium sulphate, 0.1 M citrate, pH 4.2 |
