9RJD

X-ray structure of Leptospira interrogans Histone deacetylase 11 (HDAC11) in complex with cis-dodec-5-enoic acid

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	BESSY BEAMLINE 14.1
Synchrotron site	BESSY
Beamline	14.1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2023-01-20
Detector	DECTRIS PILATUS3 S 6M
Wavelength(s)	0.9184
Spacegroup name	P 1
Unit cell lengths	48.739, 50.366, 62.175
Unit cell angles	88.49, 89.97, 79.72

Refinement procedure

Resolution	32.190 - 1.510
R-factor	0.1575
Rwork	0.156
R-free	0.18410
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.005
RMSD bond angle	0.833
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	Auto-Rickshaw
Refinement software	PHENIX ((???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	49.540	1.530
High resolution limit [Å]	1.510	1.510
Rmerge	0.058	0.518
Number of reflections	83014	2612
<I/σ(I)>	14.1	2.4
Completeness [%]	90.0	56.8
Redundancy	3.7	3.5
CC(1/2)	0.998	0.785

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	5:1:5 Precipitant: 0.1 M CaCl2, 0.1 M MgCl2, 0.1 M PIPES pH 7.0, 5.625% PEG 3350, 5.625% PEG 4000, 5.625% PEG 2000, 5.625% PEG 5000 MME Seeding stock 0.1 M HEPES pH 7.4, 0.1 M MgCl2, 0.1 M NaCl, 25% (w/v) PEG 3350 Protein in buffer: 25 mM Tris-HCl, 140 mM NaCl, 100 mM KCl, 3% glycerol, pH 8 cryoprotection: 25% glycerol in precipitant