10AI

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 N530D mutant complexed with cis-BAS-2

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	2025-12-05
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.979
Spacegroup name	P 21 21 21
Unit cell lengths	74.887, 91.654, 96.511
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	42.700 - 2.100
R-factor	0.2047
Rwork	0.203
R-free	0.23300
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	0.860
Data reduction software	XDS (Jan 19, 2025 (BUILT 20250714))
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]	42.700	2.160
High resolution limit [Å]	2.100	2.100
Rmerge	0.279	1.082
Rmeas	0.311	1.204
Rpim	0.135	0.517
Number of reflections	74093	3187
<I/σ(I)>	4.2	1.6
Completeness [%]	99.8	99.9
Redundancy	5.1	5.2
CC(1/2)	0.982	0.754

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	10 mg/mL HDAC6 protein, 2 mM inhibitor, 0.04 M Citric acid, 0.06 M BIS-TRIS propane pH 6.4, 20% w/v Polyethylene glycol 3,350