5AKS
Transthyretin binding heterogeneity and anti-amyloidogenic activity of natural polyphenols and their metabolites: resveratrol-3-O- glucuronide
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) |
Synchrotron site | PETRA III, EMBL c/o DESY |
Beamline | P13 (MX1) |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2013-08-31 |
Detector | DECTRIS PILATUS 6M |
Spacegroup name | P 21 21 2 |
Unit cell lengths | 42.806, 85.267, 63.793 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 63.793 - 1.250 |
R-factor | 0.1677 |
Rwork | 0.167 |
R-free | 0.18790 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 1f41 |
RMSD bond length | 0.021 |
RMSD bond angle | 2.044 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHENIX |
Refinement software | PHENIX ((PHENIX.REFINE)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 63.790 | 1.270 |
High resolution limit [Å] | 1.250 | 1.250 |
Rmerge | 0.040 | 0.080 |
Number of reflections | 61920 | |
<I/σ(I)> | 21.6 | 3.5 |
Completeness [%] | 95.1 | 80.2 |
Redundancy | 6.7 | 6.3 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | CRYSTALS OF WT HUMAN TTR- LIGAND COMPLEXES WERE OBTAINED AT ROOM TEMPERATURE IN ABOUT ONE WEEK BY CO-CRYSTALLIZATION, USING THE HANGING-DROP VAPOR DIFFUSION METHOD. THE PROTEIN (5 MG/ML), IN 20 MM SODIUM PHOSPHATE, PH 7, WAS INCUBATED WITH A FOUR-FOLD MOLAR EXCESS OF LIGANDS SOLUBILIZED IN DMSO. DROPS WERE FORMED BY MIXING EQUAL VOLUMES OF THE SOLUTION CONTAINING LIGAND-TTR COMPLEXES AND OF THE RESERVOIR/PRECIPITANT SOLUTION (2.2 M AMMONIUM SULPHATE, 0.1 M KCL, 0.03 M SODIUM PHOSPHATE, PH 7.0). |