6PZS

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with JR005

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SSRL BEAMLINE BL9-2
Synchrotron site	SSRL
Beamline	BL9-2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2018-11-15
Detector	DECTRIS PILATUS 6M
Wavelength(s)	0.98
Spacegroup name	P 2 21 21
Unit cell lengths	51.650, 83.670, 94.779
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	47.390 - 1.790
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5eem
Data reduction software	MOSFLM
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	47.390	1.850
High resolution limit [Å]	1.790	1.790
Rmerge	0.282	1.101
Rpim	0.123	0.527
Number of reflections	39180	3857
<I/σ(I)>	5.5	2.1
Completeness [%]	99.5	99.2
Redundancy	6.1	5.3
CC(1/2)	0.958	0.504

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	10 mg/mL zCD2 protein, 2 mM JR005 inhibitor, 0.2 lithium nitrate, 20% w/v PEG3350, 1:1 ratio protein to precipitant