6UO2
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) complexed with Trichostatin A
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 | 2019-07-08 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.98 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 53.030, 124.261, 55.520 |
Unit cell angles | 90.00, 114.09, 90.00 |
Refinement procedure
Resolution | 50.685 - 1.650 |
R-factor | 0.189023392601 |
Rwork | 0.187 |
R-free | 0.22244 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5eef |
RMSD bond length | 0.006 |
RMSD bond angle | 0.801 |
Data reduction software | iMOSFLM |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX (1.11.1_2575) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 50.685 | 1.700 |
High resolution limit [Å] | 1.650 | 1.650 |
Rmerge | 0.064 | 0.546 |
Rpim | 0.041 | 0.350 |
Number of reflections | 77846 | 7694 |
<I/σ(I)> | 9.9 | 2 |
Completeness [%] | 99.1 | |
Redundancy | 3.4 | |
CC(1/2) | 0.997 | 0.753 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 10 mg/ml HDAC6 CD1 2 mM Inhibitor 0.2 M ammonium tartrate dibasic (pH 7.0) 20% PEG 3350 1:1 protein precipitant drop ratio |