7KUT
Crystal Structure of Danio rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate)
Experimental procedure
Experimental method | SINGLE WAVELENGTH |
Source type | SYNCHROTRON |
Source details | APS BEAMLINE 24-ID-C |
Synchrotron site | APS |
Beamline | 24-ID-C |
Temperature [K] | 100 |
Detector technology | PIXEL |
Collection date | 2020-02-16 |
Detector | DECTRIS PILATUS 6M-F |
Wavelength(s) | 0.9791 |
Spacegroup name | P 31 2 1 |
Unit cell lengths | 80.248, 80.248, 245.960 |
Unit cell angles | 90.00, 90.00, 120.00 |
Refinement procedure
Resolution | 60.500 - 2.050 |
R-factor | 0.1781 |
Rwork | 0.176 |
R-free | 0.21910 |
Structure solution method | MOLECULAR REPLACEMENT |
Starting model (for MR) | 5td7 |
RMSD bond length | 0.007 |
RMSD bond angle | 0.858 |
Data reduction software | iMOSFLM |
Data scaling software | Aimless |
Phasing software | PHASER |
Refinement software | PHENIX (1.14_3260) |
Data quality characteristics
Overall | Outer shell | |
Low resolution limit [Å] | 69.500 | 2.110 |
High resolution limit [Å] | 2.050 | 2.050 |
Rmerge | 0.125 | 1.317 |
Rpim | 0.042 | 0.474 |
Number of reflections | 58731 | 5784 |
<I/σ(I)> | 11.1 | 2.1 |
Completeness [%] | 100.0 | |
Redundancy | 9.5 | |
CC(1/2) | 0.997 | 0.474 |
Crystallization Conditions
crystal ID | method | pH | temperature | details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 10 mg/mL HDAC10, 10 mM Acetylputrescine, 1:1000 trypsin:HDAC10, 0.113 M sodium phosphate monobasic, 0.068 M sodium phosphate dibasic, 18% PEG3350 (w/v), 4% (v/v) polypropylene glycol P400, HDAC10 microseed |