5GQF
Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, lacto-N-biose complex
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PHOTON FACTORY BEAMLINE AR-NW12A |
Synchrotron site | Photon Factory |
Beamline | AR-NW12A |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2015-11-03 |
Detector | ADSC QUANTUM 210 |
Wavelength(s) | 1.0 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 64.035, 143.625, 146.180 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 102.450 - 1.820 |
R-factor | 0.18218 |
Rwork | 0.181 |
R-free | 0.23575 |
Structure solution method | SAD |
RMSD bond length | 0.021 |
RMSD bond angle | 1.867 |
Data reduction software | HKL-2000 |
Data scaling software | HKL-2000 |
Phasing software | PHENIX |
Refinement software | REFMAC (5.8.0155) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 102.450 | 1.850 |
High resolution limit [Å] | 1.820 | 1.820 |
Rmerge | 0.076 | 0.736 |
Number of reflections | 116978 | |
<I/σ(I)> | 23.1 | 2 |
Completeness [%] | 96.3 | 96.5 |
Redundancy | 4.7 | 4.7 |
CC(1/2) | 0.811 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293.15 | 0.1 M ammonium fluoride, 0.1 M MES-NaOH, 20-21% (v/v) PEG3350, 5% MPD |