8BJK | pdb_00008bjk

X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with an inhibitor CPD11352

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	283	19% PEG 3350 (SIGMA-ALDRICH), 0.2 M KSCN (HAMPTON RESEARCH), 0.1 M BIS-TRIS Ph 6.5 (SIGMA-ALDRICH)

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.49	α = 90
b = 83.78	β = 90
c = 94.33	γ = 90

Symmetry
Space Group	P 2 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	Bruker PHOTON II		2021-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	BRUKER METALJET	1.34

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.35	62.64	99.9	0.12	0.125	0.032	0.999	17.9	15		90048

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.37	98.7		0.923	0.3	0.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	6r0k	1.35	62.64	85454	4531	99.91	0.17002	0.16807	0.17	0.2073	0.17	RANDOM	15.072

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]
-0.05			-0.34		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.411
r_sphericity_free	30.091
r_dihedral_angle_4_deg	17.178
r_dihedral_angle_3_deg	12.742
r_sphericity_bonded	9.421
r_dihedral_angle_1_deg	6.577
r_long_range_B_refined	2.808
r_rigid_bond_restr	2.462
r_scbond_it	1.914
r_mcangle_it	1.472
r_angle_refined_deg	1.454
r_mcbond_it	1.233
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2751
Nucleic Acid Atoms
Solvent Atoms	369
Heterogen Atoms	26

Software

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