9CBH
Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with p-Aminomethyl Phenylthioketone
This is a non-PDB format compatible entry.
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | NSLS-II BEAMLINE 17-ID-2 |
Synchrotron site | NSLS-II |
Beamline | 17-ID-2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2024-03-22 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.98 |
Spacegroup name | P 31 2 1 |
Unit cell lengths | 80.151, 80.151, 228.734 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 33.410 - 2.800 |
R-factor | 0.2285 |
Rwork | 0.224 |
R-free | 0.26910 |
Structure solution method | MOLECULAR REPLACEMENT |
RMSD bond length | 0.003 |
RMSD bond angle | 0.540 |
Data reduction software | autoPROC (1.0.5) |
Data scaling software | Aimless (0.7.13) |
Phasing software | PHASER (2.8.3) |
Refinement software | PHENIX (1.21rc1_5156) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 33.410 | 2.950 |
High resolution limit [Å] | 2.800 | 2.800 |
Rmerge | 0.221 | 2.075 |
Rpim | 0.076 | 0.722 |
Number of reflections | 21853 | 3144 |
<I/σ(I)> | 6.7 | 1.1 |
Completeness [%] | 99.9 | 100 |
Redundancy | 9.6 | 9.2 |
CC(1/2) | 0.996 | 0.523 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 10 mg/mL HDAC10 protein, 2 mM inhibitor, 0.18 M (NH4)3PO4, 0.1 M guanidine hydrochloride, 18% (w/v) PEG 3350 |