7O2R
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with ITF3985
Experimental procedure
| Experimental method | SINGLE WAVELENGTH |
| Source type | SYNCHROTRON |
| Source details | ELETTRA BEAMLINE 11.2C |
| Synchrotron site | ELETTRA |
| Beamline | 11.2C |
| Temperature [K] | 100 |
| Detector technology | PIXEL |
| Collection date | 2020-03-30 |
| Detector | DECTRIS PILATUS 6M |
| Wavelength(s) | 1.0000 |
| Spacegroup name | P 2 21 21 |
| Unit cell lengths | 51.966, 84.212, 94.977 |
| Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
| Resolution | 45.630 - 2.300 |
| R-factor | 0.2025 |
| Rwork | 0.199 |
| R-free | 0.25990 |
| Structure solution method | MOLECULAR REPLACEMENT |
| Starting model (for MR) | 5eek |
| RMSD bond length | 0.009 |
| RMSD bond angle | 1.614 |
| Data reduction software | XDS (VERSION Mar 15, 2019 BUILT=20191015) |
| Data scaling software | Aimless (0.7.4) |
| Phasing software | PHASER (2.8.3) |
| Refinement software | REFMAC (5.8.0258) |
Data quality characteristics
| Overall | Inner shell | Outer shell | |
| Low resolution limit [Å] | 47.490 | 47.490 | 2.380 |
| High resolution limit [Å] | 2.300 | 8.900 | 2.300 |
| Rmerge | 0.255 | 0.053 | 1.577 |
| Rmeas | 0.266 | 0.056 | 1.666 |
| Rpim | 0.072 | 0.017 | 0.524 |
| Total number of observations | 230764 | 4126 | 17208 |
| Number of reflections | 17684 | 395 | 1800 |
| <I/σ(I)> | 9.6 | 32.5 | 1.6 |
| Completeness [%] | 91.8 | 99.6 | 97.4 |
| Redundancy | 13 | 10.4 | 9.6 |
| CC(1/2) | 0.996 | 0.999 | 0.690 |
Crystallization Conditions
| crystal ID | method | pH | temperature | details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 277 | 0.1 M Bis-Tris propane pH 8.5, 0.2 M sodium iodide, 19% (w/v) PEG 3350 |
