6WDY
Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Indole 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 |
Wavelength(s) | 0.9791 |
Spacegroup name | P 31 2 1 |
Unit cell lengths | 80.670, 80.670, 243.980 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 69.860 - 2.650 |
R-factor | 0.1935 |
Rwork | 0.190 |
R-free | 0.25520 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5td7 |
RMSD bond length | 0.008 |
RMSD bond angle | 1.017 |
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 | 2.780 |
High resolution limit [Å] | 2.650 | 2.650 |
Rmerge | 0.187 | 1.123 |
Rpim | 0.095 | 0.570 |
Number of reflections | 27673 | 2716 |
<I/σ(I)> | 8.4 | 2.1 |
Completeness [%] | 100.0 | |
Redundancy | 9 | |
CC(1/2) | 0.996 | 0.651 |
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, 0.152 M potassium phosphate monobasic, 0.048 M potassium phosphate dibasic, and 20% PEG3350 (w/v) |