6UO5
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) Y363F mutant complexed with AR-42
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 21 21 21 |
Unit cell lengths | 54.569, 60.546, 121.972 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 60.986 - 1.439 |
R-factor | 0.17517285659 |
Rwork | 0.174 |
R-free | 0.19651 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5eef |
RMSD bond length | 0.006 |
RMSD bond angle | 0.818 |
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] | 60.986 | 1.490 |
High resolution limit [Å] | 1.439 | 1.440 |
Rmerge | 0.052 | 0.747 |
Rpim | 0.022 | 0.316 |
Number of reflections | 73858 | 7242 |
<I/σ(I)> | 19.2 | 2.2 |
Completeness [%] | 99.9 | |
Redundancy | 6.6 | |
CC(1/2) | 1.000 | 0.872 |
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 phosphate dibasic dihydride 20% PEG 3350 1:1 ratio protein to precipitant |