7U3M

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with N-methylpiperazine Benzhydroxamic Acid

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)	0.9792
Spacegroup name	P 31 2 1
Unit cell lengths	80.750, 80.750, 248.874
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	60.960 - 2.100
R-factor	0.1974
Rwork	0.196
R-free	0.23270
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5td7
RMSD bond length	0.007
RMSD bond angle	0.906
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]	60.960	2.160
High resolution limit [Å]	2.100	2.100
Rmerge	0.066	0.702
Rpim	0.055	0.412
Number of reflections	101015	15000
<I/σ(I)>	8.9	2
Completeness [%]	97.5
Redundancy	3.5
CC(1/2)	0.998	0.702

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, 0.1 M Sodium Phosphate Monobasic, 0.1 M Sodium Phosphate Dibasic, and 20% PEG 3350. Microseed crystals of HDAC10-Tubastatin were also added to the drop