6DVM
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-122
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 24-ID-E |
Synchrotron site | APS |
Beamline | 24-ID-E |
Temperature [K] | 100 |
Detector technology | CCD |
Collection date | 2017-08-01 |
Detector | ADSC QUANTUM 315 |
Wavelength(s) | 0.97918 |
Spacegroup name | P 1 21 1 |
Unit cell lengths | 78.450, 95.180, 98.030 |
Unit cell angles | 90.00, 98.87, 90.00 |
Refinement procedure
Resolution | 56.423 - 1.470 |
R-factor | 0.1489 |
Rwork | 0.148 |
R-free | 0.16980 |
RMSD bond length | 0.009 |
RMSD bond angle | 1.039 |
Data reduction software | iMOSFLM |
Data scaling software | Aimless (0.5.32) |
Phasing software | PHASER |
Refinement software | PHENIX (1.12_2829) |
Data quality characteristics
Overall | Inner shell | Outer shell | |
Low resolution limit [Å] | 67.890 | 67.890 | 1.500 |
High resolution limit [Å] | 1.470 | 8.050 | 1.470 |
Rmerge | 0.129 | 0.048 | 0.723 |
Total number of observations | 899877 | 5745 | 44887 |
Number of reflections | 238509 | 1542 | 11722 |
<I/σ(I)> | 8.2 | 17.4 | 2.8 |
Completeness [%] | 98.9 | 99.7 | 98.7 |
Redundancy | 3.8 | 3.7 | 3.8 |
CC(1/2) | 0.989 | 0.993 | 0.594 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 2% tacsimate (6.0); 0.1 M BisTris (6.5); 20 % PEG 3,350 |