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Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) Y363F mutant complexed with AR-42
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 10 mg/ml HDAC6 CD1
2 mM Inhibitor
0.2 M sodium phosphate dibasic dihydride
20% PEG 3350
1:1 ratio protein to precipitant
Crystal Properties Matthews coefficient Solvent content 2.5 50.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.569 α = 90 b = 60.546 β = 90 c = 121.972 γ = 90
Symmetry Space Group P 21 21 21
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 2019-06-08 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 1.43934220419 60.986 99.9 0.052 0.022 1 19.2 6.6 73858 16.1241389087
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 1.44 1.49 0.747 0.316 0.872 2.2
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 5EEF 1.43934220419 60.986 1.34759331692 73858 3692 99.8027133668 0.17517285659 0.174069590833 0.1765 0.196514475533 0.1981 20.6594621011
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 21.6221714817 f_angle_d 0.818484122128 f_chiral_restr 0.0765546822191 f_plane_restr 0.00581156275456 f_bond_d 0.00563049685004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2746 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing