7U6A
Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 3-thienylmethyl Benzhydroxamic Acid Inhibitor
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 | 2020-02-16 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.9792 |
Spacegroup name | P 31 2 1 |
Unit cell lengths | 80.748, 80.748, 248.919 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 60.970 - 2.250 |
R-factor | 0.1965 |
Rwork | 0.195 |
R-free | 0.22700 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5td7 |
RMSD bond length | 0.008 |
RMSD bond angle | 0.929 |
Data reduction software | iMOSFLM |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX (1.16_3549) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 60.970 | 2.330 |
High resolution limit [Å] | 2.250 | 2.250 |
Rmerge | 0.093 | 1.266 |
Rpim | 0.046 | 0.622 |
Number of reflections | 45730 | 4484 |
<I/σ(I)> | 13.8 | 2.4 |
Completeness [%] | 100.0 | |
Redundancy | 9.5 | |
CC(1/2) | 0.999 | 0.690 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 10 mg/mL HDAC10, 2 mM inhibitor, 1:1000 trypsin:HDAC10, 0.1 M Sodium Phosphate Monobasic, 0.1 M Sodium Phosphate Dibasic, and 20% PEG 3350. Microseed crystals of HDAC10-Tubastatin were also added to the drop |