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Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with spirocyclic inhibitor 20b
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 2.5 days
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.16 α = 69.686 b = 55.64 β = 87.332 c = 76.259 γ = 86.251
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 16M 2025-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979338 NSLS-II 17-ID-2
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 1.857 33.93 97.7 0.2658 0.1733 0.949 3.22 3.3 61101 8.35
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 1.86 1.9 0.7502 0.4835 0.356
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 1.86 33.93 1.99 61079 1991 97.7 0.2022 0.2009 0.201 0.242 0.2415 12.43
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 13.7034 f_angle_d 0.7197 f_chiral_restr 0.0434 f_plane_restr 0.0063 f_bond_d 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5276 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 110
Software Software Software Name Purpose PHENIX refinement autoPROC data processing