8A8Z
Crystal structure of Danio rerio HDAC6 CD2 in complex with in situ enzymatically hydrolyzed DFMO-based ITF5924
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 | 2021-03-09 |
Detector | DECTRIS PILATUS 6M |
Wavelength(s) | 1.283 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 52.372, 118.924, 60.263 |
Unit cell angles | 90.00, 93.87, 90.00 |
Refinement procedure
Resolution | 47.880 - 1.600 |
R-factor | 0.1568 |
Rwork | 0.155 |
R-free | 0.19030 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5eek |
RMSD bond length | 0.010 |
RMSD bond angle | 1.609 |
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 (5.8.0267) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 47.880 | 1.630 |
High resolution limit [Å] | 1.600 | 1.600 |
Rmerge | 0.133 | 2.494 |
Rmeas | 0.143 | |
Rpim | 0.052 | 1.356 |
Number of reflections | 92341 | 4419 |
<I/σ(I)> | 8.8 | 0.8 |
Completeness [%] | 95.6 | 91.9 |
Redundancy | 7.5 | 7.4 |
CC(1/2) | 0.998 | 0.370 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 277 | 0.1 M Na-citrate pH 6.5, 20% (v/v) PEG4000, 20% (v/v) isopropanol |