6R0K

X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with a inhibitor SS208


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.528319 % PEG 3350, 0.2 M KSCN, 0,1 M Bis Tris pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.5551.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.028α = 90
b = 93.886β = 90
c = 51.679γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90PIXELDECTRIS PILATUS 2M2019-01-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.918BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.155095.30.05515.136.8138875
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.151.22910.961.796.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5EEK1.1546.94136766210095.290.170390.170270.17823RANDOM18.587
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]
-1.632.54-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.141
r_dihedral_angle_4_deg17.036
r_dihedral_angle_3_deg12.834
r_dihedral_angle_1_deg6.557
r_long_range_B_refined4.384
r_angle_refined_deg1.646
r_scbond_it1.434
r_mcangle_it1.269
r_mcbond_it0.839
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.141
r_dihedral_angle_4_deg17.036
r_dihedral_angle_3_deg12.834
r_dihedral_angle_1_deg6.557
r_long_range_B_refined4.384
r_angle_refined_deg1.646
r_scbond_it1.434
r_mcangle_it1.269
r_mcbond_it0.839
r_chiral_restr0.103
r_gen_planes_refined0.011
r_bond_refined_d0.009
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2764
Nucleic Acid Atoms
Solvent Atoms396
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
REFMACphasing
pointlessdata scaling