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Crystal structure of fragment (3-(5-Chloro-1,3-benzothiazol-2-yl)propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C5K pdbid 3C5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.1 41.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.7 α = 90 b = 44.027 β = 90 c = 55.895 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 2016-06-06 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 1.6 34.61 100 0.064 0.07 0.027 0.999 21.8 6.7 13820
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 1.6 1.63 100 0.417 0.454 0.176 0.917 4.7 6.5 680
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 THROUGHOUT pdbid 3C5K 1.6 34.61 13143 637 99.91 0.1588 0.1572 0.1658 0.1907 0.2018 RANDOM 15.362
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] -0.18 1.25 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.336 r_dihedral_angle_4_deg 19.567 r_dihedral_angle_3_deg 12.423 r_dihedral_angle_1_deg 6.485 r_mcangle_it 2.279 r_angle_refined_deg 1.851 r_mcbond_it 1.426 r_mcbond_other 1.339 r_angle_other_deg 1.141 r_chiral_restr 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.336 r_dihedral_angle_4_deg 19.567 r_dihedral_angle_3_deg 12.423 r_dihedral_angle_1_deg 6.485 r_mcangle_it 2.279 r_angle_refined_deg 1.851 r_mcbond_it 1.426 r_mcbond_other 1.339 r_angle_other_deg 1.141 r_chiral_restr 0.123 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 782 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction