7U8Z
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with fluorinated peptoid inhibitor
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | NSLS-II BEAMLINE 17-ID-1 |
Synchrotron site | NSLS-II |
Beamline | 17-ID-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2021-11-23 |
Detector | DECTRIS EIGER X 9M |
Wavelength(s) | 0.98 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 78.340, 95.130, 98.139 |
Unit cell angles | 90.00, 98.73, 90.00 |
Refinement procedure
Resolution | 56.480 - 1.850 |
R-factor | 0.1742 |
Rwork | 0.172 |
R-free | 0.21540 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5eem |
RMSD bond length | 0.007 |
RMSD bond angle | 0.924 |
Data reduction software | iMOSFLM |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX (1.13_2998) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 56.480 | 1.916 |
High resolution limit [Å] | 1.850 | 1.850 |
Number of reflections | 205228 | 19929 |
<I/σ(I)> | 5.4 | |
Completeness [%] | 98.1 | |
Redundancy | 2.6 | |
CC(1/2) | 0.980 | 0.720 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 10 mg/mL HDAC6 protein, 2% v/v Tacsimate pH 8.0, 0.1 M Tris pH 8.5, and 16% w/v PEG 3,350 |