6UHV
Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 6-[(3-aminopropyl)amino]-N-hydroxyhexanamide
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 | 80.525, 80.525, 245.874 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 28.720 - 2.530 |
R-factor | 0.207 |
Rwork | 0.204 |
R-free | 0.24640 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5td7 |
RMSD bond length | 0.002 |
RMSD bond angle | 0.525 |
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] | 28.720 | 2.620 |
High resolution limit [Å] | 2.530 | 2.530 |
Rmerge | 0.147 | 0.664 |
Rpim | 0.070 | 0.312 |
Number of reflections | 31691 | 3068 |
<I/σ(I)> | 10.3 | 2.4 |
Completeness [%] | 99.7 | |
Redundancy | 10.1 | |
CC(1/2) | 0.995 | 0.855 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 10 mg/mL zHDAC10, 5 mM inhibitor 3, 1:1000 trypsin:zHDAC10, 0.2 M ammonium phosphate monobasic, 20% PEG3350, 0.1 M sodium citrate tribasic dihydrate, seeded with zHDAC10 microcrystals |