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Crystal structure of a low occupancy fragment candidate (N-(4-Methyl-1,3-thiazol-2-yl)propanamide) bound adjacent to 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 2015-09-30 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 1.05 34.8 97.4 0.058 0.064 0.026 0.999 14.6 5.4 47523
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 1.05 1.07 79.1 0.893 1.125 0.672 0.478 1 2.4 1876
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 1.05 34.8 45286 2178 97.2 0.1291 0.1283 0.1413 0.1464 0.1563 RANDOM 13.189
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] -0.21 0.67 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.21 r_sphericity_free 20.677 r_dihedral_angle_3_deg 11.047 r_dihedral_angle_1_deg 6.624 r_dihedral_angle_4_deg 6.14 r_sphericity_bonded 5.867 r_rigid_bond_restr 1.543 r_angle_refined_deg 1.504 r_mcangle_it 1.177 r_angle_other_deg 1.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.21 r_sphericity_free 20.677 r_dihedral_angle_3_deg 11.047 r_dihedral_angle_1_deg 6.624 r_dihedral_angle_4_deg 6.14 r_sphericity_bonded 5.867 r_rigid_bond_restr 1.543 r_angle_refined_deg 1.504 r_mcangle_it 1.177 r_angle_other_deg 1.098 r_mcbond_other 0.886 r_mcbond_it 0.862 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 779 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction