Experiment: 9RJE

X-ray structure of Chlamydomonas reinhardtii Histone Deacetylase 11 (HDAC11) in complex with hexanoic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	293.15	Precipitant: 0.1 M Bis-Tris, 0.2 M sodium nitrate, 15% PEG 3350, 15% glycerol, pH 6.6 SEC Buffer:25 mM Tris-HCl, 140 mM NaCl, 100 mM KCl, 3% glycerol, pH 8 cryoprotection: 20% glycerol in precipitant

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.66	α = 90
b = 90.04	β = 90
c = 102.97	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2025-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.04	50	97.9	0.15	0.999	13.72	12.48		174843			7.94

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.04	1.1	90.7		1.135	0.741	2.13

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.06	32.07	1.35	166617	2099	98.77	0.1425	0.1422	0.1422	0.1649	0.165	Random selection	13.68

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.8351
f_angle_d	0.7846
f_chiral_restr	0.0745
f_plane_restr	0.0092
f_bond_d	0.0039

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2434
Nucleic Acid Atoms
Solvent Atoms	552
Heterogen Atoms	35

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing