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Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with SelSA
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 zCD2 protein, 0.09 M Bis-Tris (pH 6.0), 0.18 M potassium thiocyanate, 0.01 M cadmium chloride hydrate, 18% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.29 46.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.168 α = 73.051 b = 54.19 β = 89.827 c = 74.349 γ = 82.907
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 KB bimorph mirrors 2024-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.920 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 2.15 34.32 98.3 0.224 0.194 0.765 2.2 2.1 79465 12.89
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 2.15 2.22 97.5 0.565 0.495 0.624 1 2
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 2.15 34.32 1.96 38151 1999 89.55 0.2263 0.2255 0.2256 0.24 0.2387 14.82
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 13.3221 f_angle_d 0.8081 f_chiral_restr 0.0485 f_plane_restr 0.0055 f_bond_d 0.0045
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5426 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 44
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling PHENIX refinement PHASER phasing