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Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with DKFZ-728
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 DKFZ-728, 1:1000 trypsin:HDAC10, 0.192 M Sodium Phosphate Monobasic, 0.008 M Sodium Phosphate Dibasic, and 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 3.04 59.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.548 α = 90 b = 80.548 β = 90 c = 243.35 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 2.2 69.76 99.8 0.143 0.072 0.996 9.4 9.1 47515 39.49
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 2.2 2.27 1.322 0.653 0.667 1.8
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 2.2 69.76 1.34 47429 2395 99.75 0.1977 0.1953 0.196 0.2429 0.2408 48.56
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 9.5959 f_angle_d 0.9205 f_chiral_restr 0.051 f_bond_d 0.0073 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4837 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing