6PZO
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with YX-153
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 24-ID-E |
Synchrotron site | APS |
Beamline | 24-ID-E |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2018-03-31 |
Detector | DECTRIS EIGER X 16M |
Wavelength(s) | 0.98 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 74.810, 92.580, 96.730 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 66.880 - 1.500 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5eem |
Data reduction software | MOSFLM |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 66.880 | 1.550 |
High resolution limit [Å] | 1.500 | 1.500 |
Rmerge | 0.310 | 1.566 |
Rpim | 0.088 | 0.438 |
Number of reflections | 107228 | 10523 |
<I/σ(I)> | 6.5 | 2.3 |
Completeness [%] | 99.7 | |
Redundancy | 13.2 | |
CC(1/2) | 0.994 | 0.998 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 10 mg/mL zCD2 protein, 2 mM YX-153 inhibitor, 0.2 M succinic acid, pH 7.0, 20% w/v PEG3350, 1:1 ratio protein to precipitant |