6VNR

Crystal Structure of Danio rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Bishydroxamic Acid Inhibitor

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	2017-08-01
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.98
Spacegroup name	P 1 21 1
Unit cell lengths	48.380, 107.140, 74.350
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	48.380 - 1.943
R-factor	0.164966704782
Rwork	0.163
R-free	0.21112
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	PDB 5EEM
RMSD bond length	0.006
RMSD bond angle	0.818
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]	48.380	2.010
High resolution limit [Å]	1.940	1.940
Rmerge	0.136	0.492
Rpim	0.131	0.468
Number of reflections	49180	5063
<I/σ(I)>	4.8	2.3
Completeness [%]	88.5	90.8
Redundancy	1.7	1.7
CC(1/2)	0.912	0.518

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	10 mg/mL HDAC6 protein 2 mM Inhibitor 0.02 M citrate 0.08 M Bis-Tris propane (pH 8.8) 24% w/v PEG 3350 1:1 ratio protein to precipitant