8QA7

Crystal structure of HDAC6 catalytic domain 2 from zebrafish in complex with buffer component.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5EEN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2 M NH4Cl, 20% PEG3350, 2 mM NaAc 10 mg/ml protein mixed 1:1 with well solution Cryo 20% glycerol + well solution

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.39	α = 90
b = 92.373	β = 90
c = 96.19	γ = 90

Symmetry
Space Group	P 21 21 21

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		2018-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96861	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.47	66.63	99.2	0.999	10.6	6.1		113964

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.51	1.59			0.558

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.47	66.63	108176	5628	99.09	0.21824	0.2171	0.23953	RANDOM	26.454

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]
-0.12			2.04		-1.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.919
r_dihedral_angle_4_deg	18.922
r_dihedral_angle_3_deg	12.353
r_dihedral_angle_1_deg	5.855
r_long_range_B_refined	3.761
r_long_range_B_other	3.76
r_scangle_other	2.578
r_mcangle_it	1.949
r_mcangle_other	1.949
r_scbond_it	1.623
r_scbond_other	1.623
r_angle_refined_deg	1.31
r_mcbond_it	1.245
r_mcbond_other	1.242
r_angle_other_deg	0.96
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5579
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing