5KH7
Crystal structure of fragment (3-[6-Oxo-3-(3-pyridinyl)-1(6H)-pyridazinyl]propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | ROTATING ANODE |
Source details | RIGAKU FR-E SUPERBRIGHT |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2016-05-18 |
Detector | RIGAKU SATURN A200 |
Wavelength(s) | 1.54178 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 40.719, 43.776, 55.924 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 34.470 - 1.700 |
R-factor | 0.1479 |
Rwork | 0.146 |
R-free | 0.18270 |
Starting model (for MR) | pdbid 3C5K |
RMSD bond length | 0.012 |
RMSD bond angle | 1.489 |
Data reduction software | XDS |
Data scaling software | Aimless (0.5.25) |
Refinement software | REFMAC (5.8.0151) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 34.470 | 27.960 | 1.630 |
High resolution limit [Å] | 1.600 | 8.760 | 1.600 |
Rmerge | 0.030 | 0.020 | 0.093 |
Rmeas | 0.033 | 0.022 | 0.101 |
Rpim | 0.012 | 0.009 | 0.039 |
Total number of observations | 91630 | 524 | 4366 |
Number of reflections | 13752 | ||
<I/σ(I)> | 43.5 | 71.8 | 18.2 |
Completeness [%] | 99.9 | 97 | 99.6 |
Redundancy | 6.7 | 4.9 | 6.4 |
CC(1/2) | 1.000 | 0.999 | 0.995 |
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 |