6THV
X-ray structure of the Danio rerio histone deacetylase 6 (HDAC6; catalytic domain 2) in complex with Tubastatin A
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | EMBL/DESY, HAMBURG BEAMLINE X13 |
| Synchrotron site | EMBL/DESY, HAMBURG |
| Beamline | X13 |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2019-06-24 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 0.9796 |
| Spacegroup name | P 21 21 2 |
| Unit cell lengths | 84.278, 93.713, 51.574 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 46.900 - 1.100 |
| R-factor | 0.1601 |
| Rwork | 0.160 |
| R-free | 0.16880 |
| Structure solution method | FOURIER SYNTHESIS |
| Starting model (for MR) | 5eek |
| RMSD bond length | 0.013 |
| RMSD bond angle | 1.627 |
| Data reduction software | XDS |
| Data scaling software | Aimless |
| Phasing software | REFMAC |
| Refinement software | REFMAC (5.8.0222) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 46.900 | 1.160 |
| High resolution limit [Å] | 1.100 | 1.100 |
| Rmerge | 0.075 | 0.844 |
| Number of reflections | 166560 | 26336 |
| <I/σ(I)> | 17.45 | 2.94 |
| Completeness [%] | 99.6 | |
| Redundancy | 12.3 | |
| CC(1/2) | 0.999 | 0.864 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.8 | 283 | 0.2 M KSCN, 20 % PEG 3350, 0.1 M Bis-Tris, pH5.8 |
