6WSJ
Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with cyclopeptide des4.3.1
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 | 2020-02-12 |
Detector | DECTRIS EIGER X 9M |
Wavelength(s) | 0.98 |
Spacegroup name | P 2 21 21 |
Unit cell lengths | 51.500, 84.000, 94.420 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 62.760 - 1.700 |
R-factor | 0.1551 |
Rwork | 0.154 |
R-free | 0.17640 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5eem |
RMSD bond length | 0.006 |
RMSD bond angle | 0.963 |
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] | 62.760 | 1.760 |
High resolution limit [Å] | 1.700 | 1.700 |
Rmerge | 0.126 | 0.619 |
Rpim | 0.079 | 0.413 |
Number of reflections | 45672 | 45672 |
<I/σ(I)> | 9.8 | 3.8 |
Completeness [%] | 100.0 | |
Redundancy | 6.4 | |
CC(1/2) | 0.994 | 0.845 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 10 mg/mL HDAC6 protein 0.2 M ammonium chloride and 20% polyethylene glycol (PEG) 3350 (w/v) |