9EU0 | pdb_00009eu0

Crystal structure of Danio rerio HDAC6 CD2 in complex with hydrolyzed DFMO-inhibitor (ITF7209)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	0.1% (w/v) nOctyl-b-D-glucoside, 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 21% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.71	α = 90
b = 91.56	β = 90
c = 96.13	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 EIGER X 16M		2023-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.979	SOLEIL	PROXIMA 1

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	1.86	48.065	99.9	0.997	8.67	12.9		56003

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	1.86	1.91	99.5		0.792	1.82

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.86	48.065	56003	2801	99.863	0.179	0.1765	0.1767	0.2215	0.2225	28.725

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]
-0.41			1.164		-0.754

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.522
r_dihedral_angle_2_deg	13.823
r_dihedral_angle_3_deg	13.042
r_dihedral_angle_1_deg	6.795
r_lrange_it	6.254
r_lrange_other	6.254
r_scangle_it	4.831
r_scangle_other	4.831
r_scbond_it	3.225
r_scbond_other	3.224
r_mcangle_it	3.124
r_mcangle_other	3.124
r_mcbond_it	2.247
r_mcbond_other	2.246
r_angle_refined_deg	1.633
r_angle_other_deg	0.571
r_nbd_refined	0.254
r_symmetry_xyhbond_nbd_refined	0.229
r_nbd_other	0.198
r_symmetry_nbd_other	0.19
r_symmetry_nbd_refined	0.186
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.162
r_metal_ion_refined	0.154
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_chiral_restr_other	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5573
Nucleic Acid Atoms
Solvent Atoms	389
Heterogen Atoms	69

Software

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