6UFN
Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 7-[(3-aminopropyl)amino]heptan-2-one
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 | 2019-06-05 |
Detector | DECTRIS EIGER X 9M |
Wavelength(s) | 0.92 |
Spacegroup name | P 31 2 1 |
Unit cell lengths | 80.547, 80.547, 246.201 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 28.740 - 2.700 |
R-factor | 0.1925 |
Rwork | 0.190 |
R-free | 0.22830 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5td7 |
RMSD bond length | 0.002 |
RMSD bond angle | 0.497 |
Data reduction software | iMOSFLM |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX (1.13_2998) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 28.740 | 2.800 |
High resolution limit [Å] | 2.700 | 2.700 |
Rmerge | 0.120 | 0.758 |
Rpim | 0.057 | 0.363 |
Number of reflections | 26215 | 2554 |
<I/σ(I)> | 14.5 | 2.5 |
Completeness [%] | 99.8 | |
Redundancy | 9.9 | |
CC(1/2) | 0.998 | 0.847 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 10 mg/mL zHDAC10, 5 mM inhibitor 2, 1:1000 trypsin:zHDAC10, 0.1 M potassium phosphate monobasic, 0.1 M potassium phosphate dibasic, 20% PEG3350, seeded with zHDAC10 microcrystals, one hour at room temperature |