6ZW1

X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with an inhibitor SW101

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6R0K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	283	21% PEG 3350 (Sigma-Aldrich), 0.2 M KSCN (Hampton research), 0.1 M Bis-Tris (Sigma-Aldrich) at pH 6.5.

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.933	α = 90
b = 94.158	β = 90
c = 51.487	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	PIXEL	DECTRIS PILATUS 2M		2019-01-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.918	BESSY	14.2

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	1.13	50	99.8	0.999	12.78	6.5		152836

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	1.13	1.2			0.744	1.73

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	FOURIER SYNTHESIS	THROUGHOUT	6R0K	1.13	47.08	150734	2100	99.81	0.1399	0.1396	0.1586	RANDOM	12.785

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]
-1.29			2.58		-1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.747
r_sphericity_free	31.482
r_dihedral_angle_4_deg	15.709
r_dihedral_angle_3_deg	12.439
r_sphericity_bonded	9.953
r_rigid_bond_restr	6.781
r_dihedral_angle_1_deg	6.412
r_angle_other_deg	2.055
r_angle_refined_deg	1.748
r_chiral_restr	0.106

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.747
r_sphericity_free	31.482
r_dihedral_angle_4_deg	15.709
r_dihedral_angle_3_deg	12.439
r_sphericity_bonded	9.953
r_rigid_bond_restr	6.781
r_dihedral_angle_1_deg	6.412
r_angle_other_deg	2.055
r_angle_refined_deg	1.748
r_chiral_restr	0.106
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.01
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2764
Nucleic Acid Atoms
Solvent Atoms	418
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.