6UOC

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L mutant complexed with Givinostat

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 24-ID-E
Synchrotron site	APS
Beamline	24-ID-E
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-07-08
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.98
Spacegroup name	P 21 21 21
Unit cell lengths	55.160, 60.400, 122.160
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	42.948 - 1.400
R-factor	0.152590456209
Rwork	0.152
R-free	0.16850
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5eef
RMSD bond length	0.006
RMSD bond angle	0.841
Data reduction software	iMOSFLM
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (1.11.1_2575)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	42.948	1.450
High resolution limit [Å]	1.400	1.400
Rmerge	0.094	0.359
Rpim	0.040	0.150
Number of reflections	80865	7985
<I/σ(I)>	12.4	5.6
Completeness [%]	99.7	99.7
Redundancy	6.5	6.7
CC(1/2)	0.995	0.952

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	10 mg/ml HDAC6 CD1 2 mM Inhibitor 0.2 M magnesium formate dihydrate 20% PEG 3350 1:1 ratio protein to precipitant