6UOC

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L mutant complexed with Givinostat


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5EEF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27710 mg/ml HDAC6 CD1 2 mM Inhibitor 0.2 M magnesium formate dihydrate 20% PEG 3350 1:1 ratio protein to precipitant
Crystal Properties
Matthews coefficientSolvent content
2.5351.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.16α = 90
b = 60.4β = 90
c = 122.16γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.98APS24-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.442.947647284299.70.0940.040.99512.46.58086511.016022672
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)RedundancyNumber Unique Reflections (All)
11.41.4599.70.3590.150.9525.66.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5EEF1.4000079413642.94764728421.3379235593980865404699.69179559880.1525904562090.1517394967560.1684974017415.2124829674
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d20.9435509501
f_angle_d0.841288367647
f_chiral_restr0.077647729394
f_bond_d0.00584185692849
f_plane_restr0.00583739087982
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2756
Nucleic Acid Atoms
Solvent Atoms432
Heterogen Atoms46

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing