6WDV

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Dimethylaminomethylindole Phenylhydroxamate Inhibitor

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	2019-08-02
Detector	DECTRIS PILATUS 6M-F
Wavelength(s)	0.9791
Spacegroup name	P 31 2 1
Unit cell lengths	80.670, 80.670, 246.842
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	69.860 - 2.400
R-factor	0.1837
Rwork	0.181
R-free	0.22670
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5td7
RMSD bond length	0.007
RMSD bond angle	0.930
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]	69.860	2.490
High resolution limit [Å]	2.400	2.400
Rmerge	0.135	1.111
Rpim	0.068	0.603
Number of reflections	37432	3654
<I/σ(I)>	9.7	1.9
Completeness [%]	100.0
Redundancy	9
CC(1/2)	0.995	0.557

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	10 mg/mL HDAC10, 2 mM inhibitor, 1:1000 trypsin:HDAC10, 0.135 M sodium phosphate monobasic, 0.045 M sodium phosphate dibasic, 18% PEG3350 (w/v), and 0.5% (w/v) n-dodecyl-N,N-dimethylamine-N-oxide