8D98
Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with fluorinated inhibitor 5
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 24-ID-E |
Synchrotron site | APS |
Beamline | 24-ID-E |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-12-12 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.98 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 74.923, 91.468, 96.920 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 59.280 - 1.660 |
R-factor | 0.1839 |
Rwork | 0.183 |
R-free | 0.21140 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5eem |
RMSD bond length | 0.007 |
RMSD bond angle | 0.882 |
Data reduction software | XDS |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 91.470 | 1.680 |
High resolution limit [Å] | 1.660 | 1.660 |
Number of reflections | 527507 | 23200 |
<I/σ(I)> | 16.4 | |
Completeness [%] | 99.8 | |
Redundancy | 6.7 | |
CC(1/2) | 0.999 | 0.829 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 286 | 10mg/mL HDAC6, 0.09 M Bis-tris (pH 6.0), 0.18 M KSCN, 18% polyethylene glycol (PEG) 3350, 0.4% 1,3 propanediol |