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Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with a mercaptoacetamide-based inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.04 M citrate / 0.06 M Bis-Tris propane (pH 6.4)
20% Peg 3,350
Crystal Properties Matthews coefficient Solvent content 1.95 36.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 159.01 α = 90 b = 46.46 β = 119.19 c = 96.4 γ = 90
Symmetry Space Group C 1 2 1
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 2018-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97917 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.85 84.16 98.9 0.1 0.991 7.5 3.2 52293 22.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 99.6 0.692 0.642 3.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.85 47.762 1.34 52282 2613 98.74 0.1916 0.1899 0.2259 0.2418 24.6679
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 18.203 f_angle_d 0.663 f_chiral_restr 0.045 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5472 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 79
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing