5B8D
Crystal structure of a low occupancy fragment candidate (N-(4-Methyl-1,3-thiazol-2-yl)propanamide) bound adjacent to 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 | 2015-09-30 |
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 - 1.050 |
R-factor | 0.1291 |
Rwork | 0.128 |
R-free | 0.14640 |
Starting model (for MR) | pdbid 3C5K |
RMSD bond length | 0.016 |
RMSD bond angle | 1.504 |
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] | 34.800 | 33.420 | 1.070 |
High resolution limit [Å] | 1.050 | 5.760 | 1.050 |
Rmerge | 0.058 | 0.036 | 0.893 |
Rmeas | 0.064 | 0.040 | 1.125 |
Rpim | 0.026 | 0.016 | 0.672 |
Total number of observations | 257744 | 2071 | 4539 |
Number of reflections | 47523 | ||
<I/σ(I)> | 14.6 | 49.7 | 1 |
Completeness [%] | 97.4 | 99.6 | 79.1 |
Redundancy | 5.4 | 5.7 | 2.4 |
CC(1/2) | 0.999 | 0.997 | 0.478 |
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 |