6UO4
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) Y363F mutant complexed with Trichostatin A
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 24-ID-C |
Synchrotron site | APS |
Beamline | 24-ID-C |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2019-06-08 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.98 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 52.892, 124.407, 55.630 |
Unit cell angles | 90.00, 114.46, 90.00 |
Refinement procedure
Resolution | 62.203 - 1.268 |
R-factor | 0.182294719231 |
Rwork | 0.182 |
R-free | 0.19645 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5eef |
RMSD bond length | 0.005 |
RMSD bond angle | 0.768 |
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] | 62.203 | 1.310 |
High resolution limit [Å] | 1.268 | 1.270 |
Rmerge | 0.076 | 0.578 |
Rpim | 0.048 | 0.378 |
Number of reflections | 162601 | 15378 |
<I/σ(I)> | 10.1 | 1.8 |
Completeness [%] | 94.5 | 87.9 |
Redundancy | 3.5 | 3.1 |
CC(1/2) | 0.995 | 0.731 |
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 sodium malonate (pH 7.0) 20% PEG 3350 1:1 ratio protein to precipitant |