6V79

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with NF2376

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	2019-06-08
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.98
Spacegroup name	P 1 21 1
Unit cell lengths	48.252, 108.135, 74.345
Unit cell angles	90.00, 90.01, 90.00

Refinement procedure

Resolution	74.345 - 2.040
R-factor	0.196922853602
Rwork	0.195
R-free	0.23420
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5eem
RMSD bond length	0.007
RMSD bond angle	0.926
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]	74.400	2.110
High resolution limit [Å]	2.039	2.040
Rmerge	0.174	0.767
Rpim	0.112	0.498
Number of reflections	46684	4751
<I/σ(I)>	5.6	1.3
Completeness [%]	96.2	95.8
Redundancy	3.4	3.2
CC(1/2)	0.982	0.662

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	10 mg/mL HDAC6 CD2 Protein, 2 mM NF2376 Inhibitor, 0.2 M Ammonium Phosphate Dibasic, 20% peg 3350, 1:1 ratio protein to precipitant