9CBF

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with m-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	80.411, 80.411, 236.953
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	34.350 - 2.260
R-factor	0.2363
Rwork	0.235
R-free	0.25840
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.002
RMSD bond angle	0.481
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]	34.350	2.330
High resolution limit [Å]	2.260	2.260
Rmerge	0.123	2.330
Rpim	0.043	0.770
Number of reflections	39402	3873
<I/σ(I)>	9.1	1
Completeness [%]	91.7	100
Redundancy	9.3	10
CC(1/2)	0.998	0.539

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