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Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C5K PDB entry 3C5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 297 20% PEG3350, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.02 39.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.657 α = 90 b = 36.093 β = 90 c = 88.998 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 IMAGE PLATE RIGAKU RAXIS IV++ VariMax HR 2008-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.72 50 94.5 0.073 0.073 14.1 5.8 10865 10865 22.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.72 1.78 72.5 0.231 0.231 4.26 3.1 813
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 3C5K 1.72 33.45 10213 10213 609 94.64 0.17695 0.17695 0.17382 0.1719 0.23034 0.2268 RANDOM 21.958
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 -1.31 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.527 r_dihedral_angle_4_deg 16.224 r_dihedral_angle_3_deg 11.322 r_dihedral_angle_1_deg 5.813 r_scangle_it 2.47 r_scbond_it 1.595 r_angle_refined_deg 1.191 r_mcangle_it 1.02 r_mcbond_it 0.612 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.527 r_dihedral_angle_4_deg 16.224 r_dihedral_angle_3_deg 11.322 r_dihedral_angle_1_deg 5.813 r_scangle_it 2.47 r_scbond_it 1.595 r_angle_refined_deg 1.191 r_mcangle_it 1.02 r_mcbond_it 0.612 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.093 r_symmetry_metal_ion_refined 0.039 r_metal_ion_refined 0.037 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 799 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 4
Software Software Software Name Purpose SBC-Collect data collection PHASES phasing REFMAC refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling