6WDX
Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Hydroxyethylindole Phenylhydroxamate 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 | 2020-03-04 |
Detector | DECTRIS EIGER X 9M |
Wavelength(s) | 0.9201 |
Spacegroup name | P 31 2 1 |
Unit cell lengths | 80.440, 80.440, 243.891 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 66.980 - 2.650 |
R-factor | 0.2009 |
Rwork | 0.198 |
R-free | 0.25490 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5td7 |
RMSD bond length | 0.008 |
RMSD bond angle | 1.009 |
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] | 69.660 | 2.780 |
High resolution limit [Å] | 2.650 | 2.650 |
Rmerge | 0.208 | 1.066 |
Rpim | 0.100 | 0.524 |
Number of reflections | 27467 | 2673 |
<I/σ(I)> | 8.1 | 2.2 |
Completeness [%] | 99.9 | |
Redundancy | 9.8 | |
CC(1/2) | 0.995 | 0.533 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 10 mg/mL HDAC10, 4 mM inhibitor, 1:1000 trypsin:HDAC10, 0.175 M sodium phosphate monobasic, 0.025 M sodium phosphate dibasic, and 20% PEG3350 (w/v) |