7U59

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Piperidine-4-hydroxamic acid 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	2020-02-17
Detector	DECTRIS PILATUS 6M-F
Wavelength(s)	0.9792
Spacegroup name	P 31 2 1
Unit cell lengths	80.849, 80.849, 247.467
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	60.940 - 2.180
R-factor	0.1808
Rwork	0.179
R-free	0.20980
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5td7
RMSD bond length	0.007
RMSD bond angle	0.922
Data reduction software	iMOSFLM
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (1.16_3549)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	70.020	2.250
High resolution limit [Å]	2.180	2.180
Rmerge	0.132	1.213
Rpim	0.078	0.709
Number of reflections	99611	4286
<I/σ(I)>	8.6	2
Completeness [%]	99.8
Redundancy	7
CC(1/2)	0.994	0.664

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, 0.100 M Sodium Phosphate Monobasic, 0.100 M Sodium Phosphate Dibasic, and 20% (w/v) PEG3350. Microseed crystals of HDAC10-Tubastatin A were added to the drop as well