6WYO
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) H82F F202Y double 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 | 2019-12-15 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.98 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 53.087, 123.993, 55.012 |
Unit cell angles | 90.00, 114.42, 90.00 |
Refinement procedure
Resolution | 50.090 - 2.300 |
R-factor | 0.173674284168 |
Rwork | 0.171 |
R-free | 0.23198 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | PDB 5EEF |
RMSD bond length | 0.007 |
RMSD bond angle | 0.904 |
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] | 50.100 | 2.382 |
High resolution limit [Å] | 2.300 | 2.300 |
Rmerge | 0.054 | 0.418 |
Rpim | 0.052 | 0.395 |
Number of reflections | 28350 | 2842 |
<I/σ(I)> | 8.9 | |
Completeness [%] | 98.7 | 98.4 |
Redundancy | 3.4 | 3.2 |
CC(1/2) | 0.996 | 0.792 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 294 | 10 mg/mL HDAC6 Protein 0.2 M Potassium acetate 20% peg 3350 1:1 ratio protein to precipitant solution |