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Crystal Structure of Danio rerio Histone Deacetylase 6 in Complex with p-Aminomethyl Phenylthioketone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 10 mg/mL HDAC6, 2 mM inhibitor, 0.2 M DL-malic acid (pH 7.0), 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.04 39.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.701 α = 90 b = 91.481 β = 90 c = 96.37 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 Horizontal pre-focus bimorph mirror & KB bimorph mirrors 2023-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.98 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 1.46 96.37 100 0.168 0.056 0.996 7.8 9.5 114552 10.37
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 1.46 1.49 99.6 0.948 0.329 0.794 2 8.4
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 1.46 48.19 1.33 114335 2008 99.76 0.1778 0.1776 0.1778 0.194 0.1944 13.76
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 12.2062 f_angle_d 0.9461 f_chiral_restr 0.0837 f_plane_restr 0.0109 f_bond_d 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5490 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing