6CW8
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with RTS-V5
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 | 2017-11-20 |
Detector | DECTRIS EIGER X 9M |
Wavelength(s) | 0.98 |
Spacegroup name | C 2 2 21 |
Unit cell lengths | 48.310, 128.430, 260.490 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 45.724 - 1.900 |
R-factor | 0.153 |
Rwork | 0.151 |
R-free | 0.18750 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5eem |
RMSD bond length | 0.007 |
RMSD bond angle | 0.858 |
Data reduction software | MOSFLM |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX ((1.11.1_2575)) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 64.210 | 1.940 |
High resolution limit [Å] | 1.900 | 1.900 |
Rmerge | 0.350 | 1.584 |
Rmeas | 0.372 | 1.694 |
Rpim | 0.124 | 0.592 |
Number of reflections | 64520 | 4092 |
<I/σ(I)> | 7 | |
Completeness [%] | 100.0 | 100 |
Redundancy | 8.8 | 7.8 |
CC(1/2) | 0.977 | 0.656 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 10 mg/mL ZCD2 1:1 drop ratio of protein to precipitant 0.2M lithium chloride, 20% w/v Polyethylene glycol (PEG) 3350 Crystals appeared within 2-3 days |