6WDV
Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Dimethylaminomethylindole Phenylhydroxamate 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 | 2019-08-02 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.9791 |
Spacegroup name | P 31 2 1 |
Unit cell lengths | 80.670, 80.670, 246.842 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 69.860 - 2.400 |
R-factor | 0.1837 |
Rwork | 0.181 |
R-free | 0.22670 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5td7 |
RMSD bond length | 0.007 |
RMSD bond angle | 0.930 |
Data reduction software | iMOSFLM |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX (1.14_3260) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 69.860 | 2.490 |
High resolution limit [Å] | 2.400 | 2.400 |
Rmerge | 0.135 | 1.111 |
Rpim | 0.068 | 0.603 |
Number of reflections | 37432 | 3654 |
<I/σ(I)> | 9.7 | 1.9 |
Completeness [%] | 100.0 | |
Redundancy | 9 | |
CC(1/2) | 0.995 | 0.557 |
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, 0.135 M sodium phosphate monobasic, 0.045 M sodium phosphate dibasic, 18% PEG3350 (w/v), and 0.5% (w/v) n-dodecyl-N,N-dimethylamine-N-oxide |