9CBG

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with m-Aminoethyl 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	2024-03-22
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.98
Spacegroup name	P 31 2 1
Unit cell lengths	81.072, 81.072, 240.318
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	34.790 - 2.600
R-factor	0.2203
Rwork	0.218
R-free	0.25030
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.004
RMSD bond angle	0.686
Data reduction software	autoPROC (1.0.5)
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]	34.790	2.720
High resolution limit [Å]	2.600	2.600
Rmerge	0.153	1.871
Rpim	0.055	0.651
Number of reflections	29135	3495
<I/σ(I)>	8.6	1.3
Completeness [%]	100.0	100
Redundancy	8.7	9.1
CC(1/2)	0.998	0.581

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	10 mg/mL HDAC10 protein, 2 mM inhibitor, 0.2 M KH2PO4, 20% w/v PEG 3350