10AH

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 N530D mutant complexed with trans-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	74.766, 91.445, 96.504
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	42.680 - 2.200
R-factor	0.2159
Rwork	0.213
R-free	0.25710
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	0.891
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]	42.680	2.270
High resolution limit [Å]	2.200	2.200
Rmerge	0.354	1.214
Rmeas	0.377	1.294
Rpim	0.127	0.441
Number of reflections	60818	2242
<I/σ(I)>	4.6	1.5
Completeness [%]	93.9	76.6
Redundancy	8.6	8.3
CC(1/2)	0.988	0.832

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	10 mg/mL HDAC6 protein, 2 mM inhibitor, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 2% v/v Tacsimate pH 5.0, 16% w/v Polyethylene glycol 3,350