9CBK

Crystal Structure of Danio rerio Histone Deacetylase 6 in Complex with p-Aminomethyl Phenylthioketone

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 17-ID-2
Synchrotron site	NSLS-II
Beamline	17-ID-2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-07-10
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.98
Spacegroup name	P 21 21 21
Unit cell lengths	74.701, 91.481, 96.370
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	48.190 - 1.460
R-factor	0.1778
Rwork	0.178
R-free	0.19400
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.008
RMSD bond angle	0.946
Data reduction software	iMOSFLM (7.4.0)
Data scaling software	Aimless (0.7.13)
Phasing software	PHASER (2.8.3)
Refinement software	PHENIX (1.21rc1_5156)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	96.370	1.490
High resolution limit [Å]	1.460	1.460
Rmerge	0.168	0.948
Rpim	0.056	0.329
Number of reflections	114552	5600
<I/σ(I)>	7.8	2
Completeness [%]	100.0	99.6
Redundancy	9.5	8.4
CC(1/2)	0.996	0.794

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	10 mg/mL HDAC6, 2 mM inhibitor, 0.2 M DL-malic acid (pH 7.0), 20% (w/v) PEG 3350