☰ Navigation Tabs
Crystal structure of fragment (3-[6-Oxo-3-(3-pyridinyl)-1(6H)-pyridazinyl]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 2.09 41.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.719 α = 90 b = 43.776 β = 90 c = 55.924 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 2016-05-18 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 1.6 34.47 99.9 0.03 0.033 0.012 1 43.5 6.7 13752
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 99.6 0.093 0.101 0.039 0.995 18.2 6.4 678
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT pdbid 3C5K 1.7 34.47 10932 544 99.92 0.1479 0.1461 0.1827 0.1827 RANDOM 9.628
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] -0.01 0.49 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.966 r_dihedral_angle_4_deg 15.452 r_dihedral_angle_3_deg 11.206 r_dihedral_angle_1_deg 6.388 r_angle_refined_deg 1.489 r_mcangle_it 1.237 r_angle_other_deg 1.068 r_mcbond_it 0.74 r_mcbond_other 0.74 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.966 r_dihedral_angle_4_deg 15.452 r_dihedral_angle_3_deg 11.206 r_dihedral_angle_1_deg 6.388 r_angle_refined_deg 1.489 r_mcangle_it 1.237 r_angle_other_deg 1.068 r_mcbond_it 0.74 r_mcbond_other 0.74 r_chiral_restr 0.111 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 779 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction