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Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with 3-(3-(2-(methylamino)-2-oxoethyl)-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KH3
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 2.27 45.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.87 α = 90 b = 44.04 β = 90 c = 55.87 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 CCD RIGAKU SATURN A200 2017-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54178
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 1.55 29.98 99.9 0.042 0.046 0.018 1 30.7 6.6 15157
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 1.55 1.58 100 0.254 0.279 0.112 0.974 6.1
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 1.55 29.98 14457 699 99.82 0.16154 0.16074 0.1723 0.177 0.191 RANDOM 12.136
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] 0.25 0.59 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.318 r_dihedral_angle_4_deg 13.556 r_dihedral_angle_3_deg 10.442 r_dihedral_angle_1_deg 6.714 r_long_range_B_refined 3.356 r_long_range_B_other 3.354 r_scangle_other 2.544 r_angle_refined_deg 1.85 r_scbond_other 1.712 r_scbond_it 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.318 r_dihedral_angle_4_deg 13.556 r_dihedral_angle_3_deg 10.442 r_dihedral_angle_1_deg 6.714 r_long_range_B_refined 3.356 r_long_range_B_other 3.354 r_scangle_other 2.544 r_angle_refined_deg 1.85 r_scbond_other 1.712 r_scbond_it 1.71 r_mcangle_it 1.641 r_mcangle_other 1.639 r_angle_other_deg 1.596 r_mcbond_it 1.099 r_mcbond_other 1.098 r_chiral_restr 0.111 r_bond_refined_d 0.028 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 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 89 Heterogen Atoms 24
Software Software Software Name Purpose Aimless data scaling REFMAC refinement xia2 data reduction