☰ Navigation Tabs
X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with a inhibitor SS208
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, HANGING DROP 6.5 283 19 % PEG 3350, 0.2 M KSCN, 0,1 M Bis Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.55 51.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.028 α = 90 b = 93.886 β = 90 c = 51.679 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 90 PIXEL DECTRIS PILATUS 2M 2019-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.15 50 95.3 0.055 15.13 6.8 138875
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.22 91 0.96 1.79 6.5
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 1.15 46.94 136766 2100 95.29 0.17039 0.17027 0.173 0.17823 0.1793 RANDOM 18.587
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] -1.63 2.54 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.141 r_dihedral_angle_4_deg 17.036 r_dihedral_angle_3_deg 12.834 r_dihedral_angle_1_deg 6.557 r_long_range_B_refined 4.384 r_angle_refined_deg 1.646 r_scbond_it 1.434 r_mcangle_it 1.269 r_mcbond_it 0.839 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.141 r_dihedral_angle_4_deg 17.036 r_dihedral_angle_3_deg 12.834 r_dihedral_angle_1_deg 6.557 r_long_range_B_refined 4.384 r_angle_refined_deg 1.646 r_scbond_it 1.434 r_mcangle_it 1.269 r_mcbond_it 0.839 r_chiral_restr 0.103 r_gen_planes_refined 0.011 r_bond_refined_d 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2764 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction REFMAC phasing pointless data scaling