6WDY

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Indole 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
Wavelength(s)	0.9791
Spacegroup name	P 31 2 1
Unit cell lengths	80.670, 80.670, 243.980
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	69.860 - 2.650
R-factor	0.1935
Rwork	0.190
R-free	0.25520
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5td7
RMSD bond length	0.008
RMSD bond angle	1.017
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	2.780
High resolution limit [Å]	2.650	2.650
Rmerge	0.187	1.123
Rpim	0.095	0.570
Number of reflections	27673	2716
<I/σ(I)>	8.4	2.1
Completeness [%]	100.0
Redundancy	9
CC(1/2)	0.996	0.651

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, 0.152 M potassium phosphate monobasic, 0.048 M potassium phosphate dibasic, and 20% PEG3350 (w/v)