Experiment: 6WYQ

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L mutant complexed with 4-iodo-SAHA

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	10 mg/mL HDAC6 Protein 0.2 M Magnesium Chloride Hexahydrate 20% PEG 3350 1:1 ratio protein to precipitant solution

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.05	α = 90
b = 123.79	β = 113.52
c = 55.1	γ = 90

Symmetry
Space Group	P 1 21 1

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 EIGER X 16M		2019-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.98	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.9	39.14	77.9	0.091	0.071	0.981	5.2	2.4		39267			15.2573554585

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.968			0.271	0.231	0.829	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB 5EEF	1.90001463957	39.138993555	1.34352191654	39265	1857	76.6984412236	0.178405609415	0.176206475716	0.1767	0.222815788506	0.2234	14.5873909685

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	7.99245418393
f_angle_d	0.845858325271
f_chiral_restr	0.0518465299832
f_bond_d	0.00672480040019
f_plane_restr	0.0053777782887

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5329
Nucleic Acid Atoms
Solvent Atoms	268
Heterogen Atoms	46

Software

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