6CED
Crystal structure of fragment 3-(3-Methyl-4-oxo-3,4-dihydroquinazolin-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 | 2017-05-18 |
Detector | RIGAKU SATURN A200 |
Wavelength(s) | 1.54178 |
Spacegroup name | P 21 21 21 |
Unit cell lengths | 40.720, 44.430, 55.710 |
Unit cell angles | 90.00, 90.00, 90.00 |
Refinement procedure
Resolution | 34.740 - 1.700 |
R-factor | 0.1547 |
Rwork | 0.153 |
R-free | 0.19080 |
Starting model (for MR) | pdbid 5KH3 |
RMSD bond length | 0.022 |
RMSD bond angle | 1.785 |
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] | 34.740 | 34.740 | 1.730 |
High resolution limit [Å] | 1.700 | 9.000 | 1.700 |
Rmerge | 0.034 | 0.020 | 0.225 |
Rmeas | 0.037 | 0.023 | 0.255 |
Rpim | 0.014 | 0.009 | 0.116 |
Total number of observations | 76686 | 513 | 2466 |
Number of reflections | 11530 | 99 | 557 |
<I/σ(I)> | 38.8 | 96 | 6.6 |
Completeness [%] | 99.5 | 99.6 | 96.4 |
Redundancy | 6.7 | 5.2 | 4.4 |
CC(1/2) | 1.000 | 1.000 | 0.970 |
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 |