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Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Inhibitor 14
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TD7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 10 mg/mL HDAC10, 2 mM Inhibitor 14, 1:1000 trypsin:HDAC10, 0.131 M Sodium Phosphate Monobasic, 0.044 M Sodium Phosphate Dibasic, 3% (v/v) glycerol, and 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 3.07 59.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.5 α = 90 b = 80.5 β = 90 c = 246.632 γ = 120
Symmetry Space Group P 31 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 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97911 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 2.15 69.71 100 0.136 0.068 0.994 10.8 9.3 51497 34.1
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 2.21 1.168 0.631 0.574 2.1
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 5TD7 2.15 69.71 1.34 51497 2671 99.96 0.1916 0.1899 0.19 0.2223 0.2223 40.33
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 23.3035 f_angle_d 0.898 f_chiral_restr 0.0506 f_bond_d 0.0073 f_plane_restr 0.0061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4814 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing