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Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with spirocyclic inhibitor 14
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 2.0 mM inhibitor at 286 K for 6 days
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.178 α = 68.797 b = 55.402 β = 87.471 c = 75.855 γ = 83.06
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 2025-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.919689 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 2.097 33.18 98.03 0.3121 0.2112 0.905 2.43 3 41826 11.85
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 2.1 2.15 1.032 0.6915 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 2.1 33.18 1.97 41668 2001 98.03 0.2127 0.2114 0.2111 0.2398 0.2393 13.77
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 14.1308 f_angle_d 0.837 f_chiral_restr 0.0417 f_plane_restr 0.005 f_bond_d 0.0032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5351 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 86
Software Software Software Name Purpose PHENIX refinement autoPROC data processing