6UFO
Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 7-[(3-aminopropyl)amino]-1-methoxyheptan-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 | 80.850, 80.850, 247.025 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 28.840 - 2.680 |
R-factor | 0.1975 |
Rwork | 0.195 |
R-free | 0.23460 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5td7 |
RMSD bond length | 0.002 |
RMSD bond angle | 0.499 |
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] | 28.840 | 2.780 |
High resolution limit [Å] | 2.680 | 2.680 |
Rmerge | 0.154 | 0.860 |
Rpim | 0.073 | 0.421 |
Number of reflections | 27000 | 2553 |
<I/σ(I)> | 10.5 | 2.2 |
Completeness [%] | 99.7 | |
Redundancy | 9.9 | |
CC(1/2) | 0.993 | 0.806 |
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, 0.1 M potassium phosphate monobasic, 0.1 M potassium phosphate dibasic, 20% PEG3350, seeded with zHDAC10 microcrystals, one hour at room temperature |