8EQI
Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with cyclopeptide des4.2.0
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 | 2020-03-04 |
| Detector | DECTRIS EIGER X 9M |
| Wavelength(s) | 0.98 |
| Spacegroup name | P 21 21 21 |
| Unit cell lengths | 57.450, 92.030, 153.200 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 78.890 - 2.000 |
| R-factor | 0.2374 |
| Rwork | 0.235 |
| R-free | 0.27210 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | PDB: 5EEM |
| RMSD bond length | 0.007 |
| RMSD bond angle | 0.931 |
| Data reduction software | iMOSFLM |
| Data scaling software | Aimless |
| Phasing software | PHASER |
| Refinement software | PHENIX (1.20.1_4487) |
Data quality characteristics
| Overall | Outer shell | |
| Low resolution limit [Å] | 78.890 | 2.070 |
| High resolution limit [Å] | 2.000 | 2.000 |
| Rmerge | 0.256 | 1.037 |
| Rpim | 0.115 | 0.471 |
| Number of reflections | 111093 | 10837 |
| <I/σ(I)> | 9.1 | |
| Completeness [%] | 100.0 | |
| Redundancy | 6.4 | |
| CC(1/2) | 0.979 | 0.610 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 277 | 100nL of 10mg/mL HDAC6 with 100nL precipitant (0.2 M ammonium tartrate dibasic pH 7.0, 20% w/v polyethylene glycol 3,350) followed by 25 nL of precipitant solution containing crystal seeds of the HDAC6 complex with octapeptide inhibitor des4.3.1 |
