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X-ray structure of the Danio rerio histone deacetylase 6 (HDAC6; catalytic domain 2) in complex with Tubastatin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.8 283 0.2 M KSCN,
20 % PEG 3350,
0.1 M Bis-Tris, pH5.8
Crystal Properties Matthews coefficient Solvent content 2.55 51.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.278 α = 90 b = 93.713 β = 90 c = 51.574 γ = 90
Symmetry Space Group P 21 21 2
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 2019-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.9796 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.1 46.9 99.6 0.075 0.999 17.45 12.3 166560
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.16 0.844 0.864 2.94
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5EEK 1.1 46.9 164453 2101 99.6 0.1601 0.1599 0.1668 0.1688 0.1744 RANDOM 12.911
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] -0.79 0.94 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.574 r_dihedral_angle_4_deg 16.381 r_dihedral_angle_3_deg 11.961 r_dihedral_angle_1_deg 6.027 r_angle_other_deg 3.633 r_angle_refined_deg 1.627 r_mcangle_it 1.466 r_mcbond_it 1.129 r_mcbond_other 1.001 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.574 r_dihedral_angle_4_deg 16.381 r_dihedral_angle_3_deg 11.961 r_dihedral_angle_1_deg 6.027 r_angle_other_deg 3.633 r_angle_refined_deg 1.627 r_mcangle_it 1.466 r_mcbond_it 1.129 r_mcbond_other 1.001 r_chiral_restr 0.114 r_bond_refined_d 0.013 r_gen_planes_other 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2764 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling REFMAC phasing Coot model building