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Crystal structure of a low occupancy fragment candidate (5-[(4-Isopropylphenyl)amino]-6-methyl-1,2,4-triazin-3(2H)-one) 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 2.17 43.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.434 α = 90 b = 44.157 β = 90 c = 56.549 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 PILATUS 6M-F 2015-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 1.07 34.81 99.4 0.062 0.069 0.028 0.999 13.5 5.5 46238
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 1.07 1.1 96.6 0.957 1.1 3.1
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 1.07 34.8 44074 2104 99.29 0.1363 0.1356 0.1503 0.1574 RANDOM 14.755
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] -0.75 -0.4 1.15
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.838 r_dihedral_angle_2_deg 32.088 r_sphericity_bonded 16.791 r_dihedral_angle_3_deg 11.439 r_dihedral_angle_4_deg 8.94 r_dihedral_angle_1_deg 6.316 r_rigid_bond_restr 2.231 r_mcangle_it 1.978 r_angle_refined_deg 1.615 r_mcbond_it 1.432
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.838 r_dihedral_angle_2_deg 32.088 r_sphericity_bonded 16.791 r_dihedral_angle_3_deg 11.439 r_dihedral_angle_4_deg 8.94 r_dihedral_angle_1_deg 6.316 r_rigid_bond_restr 2.231 r_mcangle_it 1.978 r_angle_refined_deg 1.615 r_mcbond_it 1.432 r_mcbond_other 1.43 r_angle_other_deg 1.111 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 778 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 58
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction