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Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with spirocyclic inhibitor 20a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 286 10 mg/mL HDAC6 protein [in 50 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (pH 7.5), 100 mM KCl, 5% glycerol, 1 mM tris(2-carboxyethyl)phosphine] added to precipitate solution [0.1 M bis-tris (pH 6.0), 0.2 M KSCN, 20% polyethylene glycol 3350]. soaked in 1.5 mM inhibitor at 286 K for 3 days
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.487 α = 69.834 b = 55.533 β = 87.471 c = 75.767 γ = 86.537
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 9M 2025-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.919921 NSLS-II 17-ID-1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.032 34.62 98.04 0.2596 0.1587 0.954 3.78 3.7 46906 20.74
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) Redundancy Number Unique Reflections (All) 1 2.032 2.08 1.439 0.8827 0.373
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.032 34.62 1.96 46745 2021 98.04 0.2286 0.2271 0.2276 0.2629 0.262 24.54
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 Key Refinement Restraint Deviation f_dihedral_angle_d 15.6797 f_angle_d 0.8943 f_chiral_restr 0.0435 f_plane_restr 0.0068 f_bond_d 0.0039
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5376 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 108
Software Software Software Name Purpose PHENIX refinement autoPROC data processing