5KH9
Crystal structure of a low occupancy fragment candidate (5-[(4-Isopropylphenyl)amino]-6-methyl-1,2,4-triazin-3(2H)-one) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | DIAMOND BEAMLINE I04-1 |
Synchrotron site | Diamond |
Beamline | I04-1 |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2015-10-02 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.92819 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 41.434, 44.157, 56.549 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 34.800 - 1.070 |
R-factor | 0.1363 |
Rwork | 0.136 |
R-free | 0.15030 |
Starting model (for MR) | pdbid 3C5K |
RMSD bond length | 0.015 |
RMSD bond angle | 1.615 |
Data reduction software | XDS |
Data scaling software | Aimless (0.5.26) |
Refinement software | REFMAC (5.8.0151) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 34.810 | 34.810 | 1.100 |
High resolution limit [Å] | 1.070 | 4.790 | 1.070 |
Rmerge | 0.062 | 0.041 | 0.957 |
Rmeas | 0.069 | ||
Rpim | 0.028 | ||
Total number of observations | 256160 | ||
Number of reflections | 46238 | ||
<I/σ(I)> | 13.5 | 45 | 1.1 |
Completeness [%] | 99.4 | 99.8 | 96.6 |
Redundancy | 5.5 | 5.6 | 3.1 |
CC(1/2) | 0.999 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 291 | 2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol |