9MQP

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

This is a non-PDB format compatible entry.

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	2024-10-28
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.920
Spacegroup name	P 1
Unit cell lengths	48.168, 54.190, 74.349
Unit cell angles	73.05, 89.83, 82.91

Refinement procedure

Resolution	34.320 - 2.150
R-factor	0.2263
Rwork	0.226
R-free	0.24000
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.004
RMSD bond angle	0.808
Data reduction software	XDS (Jun 30, 2024 (BUILT 20241002))
Data scaling software	Aimless (0.7.9)
Phasing software	PHASER (2.8.3)
Refinement software	PHENIX (1.21.2_5419)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	34.320	2.220
High resolution limit [Å]	2.150	2.150
Rmerge	0.224	0.565
Rpim	0.194	0.495
Number of reflections	79465	6476
<I/σ(I)>	2.2	1
Completeness [%]	98.3	97.5
Redundancy	2.1	2
CC(1/2)	0.765	0.624

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	10 mg/mL HDAC6 zCD2 protein, 0.09 M Bis-Tris (pH 6.0), 0.18 M potassium thiocyanate, 0.01 M cadmium chloride hydrate, 18% (w/v) PEG 3350