9GGK | pdb_00009ggk

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) in complex with N-((6-(Hydroxyamino)-6-oxohexyl)oxy)-4-(4-methoxyphenyl)thiazole-2-carboxamide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1 M sodium acetate, 0.1 sodium formate, 28% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.278	α = 90
b = 87.098	β = 90
c = 179.771	γ = 90

Symmetry
Space Group	C 2 2 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 4M		2024-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.967700	ESRF	MASSIF-3

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	1.9	44.983	94.6	0.995	9.4	7.5		25240

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	1.9	1.94	90.6		0.453		6.8

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	1.9	44.983	25189	1260	94.172	0.211	0.208	0.2007	0.2672	0.2592	27.23

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]
0.196			-0.852		0.656

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.394
r_dihedral_angle_3_deg	13.204
r_dihedral_angle_2_deg	10.945
r_dihedral_angle_1_deg	6.715
r_lrange_it	6.125
r_scangle_it	4.818
r_scbond_it	3.202
r_mcangle_it	3.092
r_mcbond_it	2.15
r_angle_refined_deg	1.876
r_nbtor_refined	0.314
r_nbd_refined	0.215
r_symmetry_nbd_refined	0.214
r_symmetry_xyhbond_nbd_refined	0.168
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.114
r_metal_ion_refined	0.043
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2744
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	30

Software

Software
Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement