8EQI

Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with cyclopeptide des4.2.0

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 17-ID-1
Synchrotron site	NSLS-II
Beamline	17-ID-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-03-04
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.98
Spacegroup name	P 21 21 21
Unit cell lengths	57.450, 92.030, 153.200
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	78.890 - 2.000
R-factor	0.2374
Rwork	0.235
R-free	0.27210
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	PDB: 5EEM
RMSD bond length	0.007
RMSD bond angle	0.931
Data reduction software	iMOSFLM
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (1.20.1_4487)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	78.890	2.070
High resolution limit [Å]	2.000	2.000
Rmerge	0.256	1.037
Rpim	0.115	0.471
Number of reflections	111093	10837
<I/σ(I)>	9.1
Completeness [%]	100.0
Redundancy	6.4
CC(1/2)	0.979	0.610

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	100nL of 10mg/mL HDAC6 with 100nL precipitant (0.2 M ammonium tartrate dibasic pH 7.0, 20% w/v polyethylene glycol 3,350) followed by 25 nL of precipitant solution containing crystal seeds of the HDAC6 complex with octapeptide inhibitor des4.3.1