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Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with SGC-UBD253 chemical probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 2 M sodium formate, 0.2 M sodium acetate pH4.6, 5 % ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.13 42.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.61 α = 90 b = 44.91 β = 90 c = 55.7 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 EIGER X 16M 2019-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.62 55.7 99.7 0.061 0.066 0.024 0.999 14.6 7.1 13460
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.65 99.2 0.586 0.629 0.227 0.923 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 1.62 34.96 12739 681 99.62 0.16162 0.16003 0.1668 0.19036 0.1879 RANDOM 29.165
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] -0.26 2.07 -1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.193 r_dihedral_angle_4_deg 18.904 r_dihedral_angle_3_deg 13.038 r_dihedral_angle_1_deg 6.765 r_long_range_B_other 5.97 r_long_range_B_refined 5.963 r_scangle_other 5.122 r_scbond_other 3.473 r_scbond_it 3.468 r_mcangle_it 3.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.193 r_dihedral_angle_4_deg 18.904 r_dihedral_angle_3_deg 13.038 r_dihedral_angle_1_deg 6.765 r_long_range_B_other 5.97 r_long_range_B_refined 5.963 r_scangle_other 5.122 r_scbond_other 3.473 r_scbond_it 3.468 r_mcangle_it 3.183 r_mcangle_other 3.18 r_mcbond_it 2.324 r_mcbond_other 2.321 r_angle_refined_deg 1.671 r_angle_other_deg 1.518 r_chiral_restr 0.106 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 771 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction