6WDW

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

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 17-ID-1
Synchrotron site	NSLS-II
Beamline	17-ID-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-03-04
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.9201
Spacegroup name	P 31 2 1
Unit cell lengths	80.563, 80.563, 246.907
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	67.140 - 2.200
R-factor	0.202
Rwork	0.200
R-free	0.23620
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5td7
RMSD bond length	0.007
RMSD bond angle	0.955
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]	69.770	2.270
High resolution limit [Å]	2.200	2.200
Rmerge	0.232	1.758
Rpim	0.113	0.849
Number of reflections	48257	4740
<I/σ(I)>	7.1	2
Completeness [%]	100.0
Redundancy	9.6
CC(1/2)	0.996	0.646

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	10 mg/mL HDAC10, 4 mM inhibitor, 1:1000 trypsin:HDAC10, 0.168 M potassium phosphate monobasic, 0.032 M potassium phosphate dibasic, and 20% PEG3350 (w/v)