9GGH | pdb_00009ggh

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) in complex with N-((6-(Hydroxyamino)-6-oxohexyl)oxy)-4-(4-(pyrrolidin-1-yl)phenyl)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 M sodium formate, 22 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.711	α = 90
b = 87.033	β = 90
c = 178.864	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		2024-01-31	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	2.14	44.76	99.7	0.994	6.5	7.5		18936

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	2.14	2.2			0.203

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.14	44.76	17948	947	99.67	0.2094	0.20751	0.2121	0.24722	0.251	RANDOM	41.061

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]
-2.95			-1.8		4.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.789
r_dihedral_angle_1_deg	6.971
r_dihedral_angle_2_deg	6.914
r_long_range_B_refined	2.394
r_long_range_B_other	2.392
r_angle_refined_deg	1.01
r_mcangle_it	0.49
r_mcangle_other	0.49
r_scangle_other	0.437
r_angle_other_deg	0.393
r_mcbond_it	0.27
r_mcbond_other	0.27
r_scbond_it	0.243
r_scbond_other	0.243
r_chiral_restr	0.046
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2759
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	34

Software

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