6DVO
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with Bavarostat
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | SSRL BEAMLINE BL9-2 |
Synchrotron site | SSRL |
Beamline | BL9-2 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2017-06-15 |
Detector | DECTRIS PILATUS3 6M |
Wavelength(s) | 0.97946 |
Spacegroup name | P 65 |
Unit cell lengths | 97.230, 97.230, 78.900 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 42.102 - 1.980 |
R-factor | 0.1706 |
Rwork | 0.168 |
R-free | 0.21580 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5eem |
RMSD bond length | 0.004 |
RMSD bond angle | 0.714 |
Data reduction software | iMOSFLM |
Data scaling software | Aimless (0.5.32) |
Phasing software | PHASER |
Refinement software | PHENIX (1.12_2829) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 84.200 | 84.200 | 2.030 |
High resolution limit [Å] | 1.980 | 9.070 | 1.980 |
Rmerge | 0.312 | 0.058 | 1.740 |
Total number of observations | 282074 | 3578 | 19863 |
Number of reflections | 29613 | 337 | 2079 |
<I/σ(I)> | 8 | 31.3 | 1.9 |
Completeness [%] | 100.0 | 99.9 | 100 |
Redundancy | 9.5 | 10.6 | 9.6 |
CC(1/2) | 0.990 | 0.999 | 0.655 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 200 mM L-proline; 100 mM HEPES (pH 7.5); 24% PEG 1,500 |