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Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) H82F F202Y double mutant complexed with Trichostatin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEF PDB 5EEF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 10 mg/mL HDAC6 Protein
0.2 M Potassium acetate
20% peg 3350
1:1 ratio protein to precipitant solution
Crystal Properties Matthews coefficient Solvent content 2.04 39.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.087 α = 90 b = 123.993 β = 114.421 c = 55.012 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M-F 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C
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 2.3 50.1 98.7 0.054 0.052 0.996 8.9 3.4 28350 32.5564079678
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 2.3 2.382 98.4 0.418 0.395 0.792 3.2
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 5EEF 2.30000278768 50.090196779 1.38501881023 28350 1473 98.5435712051 0.173674284168 0.170581866721 0.1731 0.231983322559 0.2334 33.0078730162
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 6.63641940723 f_angle_d 0.903964961249 f_chiral_restr 0.0504531411741 f_bond_d 0.00732537059704 f_plane_restr 0.0055723465874
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5276 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing