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Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with DKFZ-711
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-711, 1:1000 trypsin:HDAC10, 0.100 M Potassium Phosphate Monobasic, 0.100 M Potassium Phosphate Dibasic, and 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 3.09 60.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.408 α = 90 b = 80.408 β = 90 c = 248.27 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 69.84 100 0.102 0.05 0.998 13 9.5 51724 40.65
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 1.119 0.569 0.639 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 69.64 1.34 51724 2622 99.99 0.1834 0.1816 0.1829 0.2159 0.218 47.73
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 6.6418 f_angle_d 0.8678 f_chiral_restr 0.051 f_bond_d 0.0073 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4862 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing