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Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with fluorinated inhibitor 10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEM PDB Entry 5EEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 286 10mg/mL HDAC6, 0.09 M Bis-tris (pH 6.0), 0.18 M KSCN, 18% PEG 3350, 0.4% tert-butanol
Crystal Properties Matthews coefficient Solvent content 2.07 40.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.023 α = 90 b = 92.02 β = 90 c = 96.545 γ = 90
Symmetry Space Group P 21 21 21
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 2021-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.98 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.82 96.54 97.7 0.999 20.4 6.4 380701 18.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.86 0.943
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB Entry 5EEM 1.82 66.61 1.34 59253 1997 97.48 0.1793 0.178 0.1782 0.2151 0.2153 19.79
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 21.9021 f_angle_d 0.8842 f_chiral_restr 0.0552 f_plane_restr 0.0083 f_bond_d 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5431 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing