6WYQ
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L mutant complexed with 4-iodo-SAHA
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 | 2019-11-02 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.98 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 53.050, 123.790, 55.100 |
Unit cell angles | 90.00, 113.52, 90.00 |
Refinement procedure
Resolution | 39.139 - 1.900 |
R-factor | 0.178405609415 |
Rwork | 0.176 |
R-free | 0.22282 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | PDB 5EEF |
RMSD bond length | 0.007 |
RMSD bond angle | 0.846 |
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] | 39.140 | 1.968 |
High resolution limit [Å] | 1.900 | 1.900 |
Rmerge | 0.091 | 0.271 |
Rpim | 0.071 | 0.231 |
Number of reflections | 39267 | 3884 |
<I/σ(I)> | 5.2 | 2 |
Completeness [%] | 77.9 | |
Redundancy | 2.4 | |
CC(1/2) | 0.981 | 0.829 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 294 | 10 mg/mL HDAC6 Protein 0.2 M Magnesium Chloride Hexahydrate 20% PEG 3350 1:1 ratio protein to precipitant solution |