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Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with NF2657
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEM PDB Entry 5EEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 10 mg/mL HDAC6 CD2 Protein,
2 mM NF2657 Inhibitor,
4% Tascimate (pH 6.0),
12% PEG 3350,
1:1 ratio protein to precipitant
Crystal Properties Matthews coefficient Solvent content 2.61 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.461 α = 90 b = 64.871 β = 90 c = 142.393 γ = 90
Symmetry Space Group P 2 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 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 2.08 71.2 99.7 0.186 0.081 0.992 10.6 6.3 25731 27.2981138944
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 2.09 2.16 97.9 1.06 0.451 0.584 1.8 6.4
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 PDB Entry 5EEM 2.08741757573 71.1965 1.36073871281 25731 1314 99.6475873286 0.195541735014 0.193184634264 0.2012 0.239064574987 0.2494 28.1080198059
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 11.023719118 f_angle_d 0.908357523166 f_chiral_restr 0.0507887451874 f_bond_d 0.00688468183066 f_plane_restr 0.00585144125988
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2750 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing