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Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with 5-[(3-aminopropyl)amino]pentylboronic acid
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 zHDAC10, 5 mM inhibitor 4, 1:1000 trypsin:zHDAC10, 0.15 M potassium phosphate monobasic, 0.05 M potassium phosphate dibasic, 20% PEG3350, seeded with zHDAC10 microcrystals
Crystal Properties Matthews coefficient Solvent content 3.06 59.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.55 α = 90 b = 80.55 β = 90 c = 244.817 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 9M 2019-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92 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 2.8 69.76 100 0.348 0.18 0.953 8.5 9.2 23533 41.66
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 2.8 2.901 1.8 0.974 0.502 3.3
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 2.8 60.61 1.33 23532 1203 99.9 0.1992 0.1962 0.1976 0.254 0.2517 40.06
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 5.8959 f_angle_d 0.6088 f_chiral_restr 0.0417 f_plane_restr 0.0039 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4817 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing