9CBH

Crystal Structure of Danio rerio Histone Deacetylase 10 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	2024-03-22
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.98
Spacegroup name	P 31 2 1
Unit cell lengths	80.151, 80.151, 228.734
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	33.410 - 2.800
R-factor	0.2285
Rwork	0.224
R-free	0.26910
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.003
RMSD bond angle	0.540
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]	33.410	2.950
High resolution limit [Å]	2.800	2.800
Rmerge	0.221	2.075
Rpim	0.076	0.722
Number of reflections	21853	3144
<I/σ(I)>	6.7	1.1
Completeness [%]	99.9	100
Redundancy	9.6	9.2
CC(1/2)	0.996	0.523

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	10 mg/mL HDAC10 protein, 2 mM inhibitor, 0.18 M (NH4)3PO4, 0.1 M guanidine hydrochloride, 18% (w/v) PEG 3350