6CEA
Crystal structure of fragment 3-(quinolin-2-yl)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 | 2015-12-16 |
Detector | RIGAKU SATURN A200 |
Wavelength(s) | 1.54178 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 40.680, 44.220, 55.960 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 32.900 - 1.600 |
R-factor | 0.1655 |
Rwork | 0.164 |
R-free | 0.19790 |
Starting model (for MR) | pdbid 5KH3 |
RMSD bond length | 0.020 |
RMSD bond angle | 2.008 |
Data reduction software | xia2 |
Data scaling software | Aimless (0.6.2) |
Refinement software | REFMAC (5.8.0189) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 32.900 | 32.900 | 1.630 |
High resolution limit [Å] | 1.600 | 8.760 | 1.600 |
Rmerge | 0.033 | 0.021 | 0.127 |
Rmeas | 0.036 | 0.023 | 0.137 |
Rpim | 0.014 | 0.009 | 0.052 |
Total number of observations | 92869 | 550 | 4501 |
Number of reflections | 13550 | 107 | 653 |
<I/σ(I)> | 35.4 | 56.8 | 14 |
Completeness [%] | 97.9 | 97.7 | 95.3 |
Redundancy | 6.9 | 5.1 | 6.9 |
CC(1/2) | 1.000 | 1.000 | 0.994 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 291 | 2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol |