7KUQ

Crystal Structure of Danio rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 24-ID-C
Synchrotron site	APS
Beamline	24-ID-C
Temperature [K]	100
Detector technology	PIXEL
Collection date	2020-02-16
Detector	DECTRIS PILATUS 6M-F
Wavelength(s)	0.9791
Spacegroup name	P 31 2 1
Unit cell lengths	80.509, 80.509, 249.380
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	60.850 - 2.100
R-factor	0.207
Rwork	0.205
R-free	0.24730
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5td7
RMSD bond length	0.007
RMSD bond angle	0.926
Data reduction software	iMOSFLM
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX (1.14_3260)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	69.720	2.160
High resolution limit [Å]	2.100	2.100
Rmerge	0.217	1.136
Rpim	0.084	0.437
Number of reflections	55699	5526
<I/σ(I)>	5.5	2.1
Completeness [%]	99.7
Redundancy	7.2
CC(1/2)	0.985	0.062

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		277	10 mg/mL HDAC10, 10 mM N8-Acetylspermidine, 1:1000 trypsin:HDAC10, 0.125 M sodium phosphate dibasic, 0.075 M sodium phosphate monobasic, 20% PEG3350 (w/v), HDAC10 microseed