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Crystal structure of Danio rerio HDAC6 CD2 in complex with hydrolyzed DFMO-inhibitor (ITF7209)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 0.1% (w/v) nOctyl-b-D-glucoside, 0.1 M
Sodium citrate tribasic dihydrate pH 5.5, 21% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.71 α = 90 b = 91.56 β = 90 c = 96.13 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 EIGER X 16M 2023-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.979 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.86 48.065 99.9 0.997 8.67 12.9 56003
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.91 99.5 0.792 1.82
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.86 48.065 56003 2801 99.863 0.179 0.1765 0.1767 0.2215 0.2225 28.725
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] -0.41 1.164 -0.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.522 r_dihedral_angle_2_deg 13.823 r_dihedral_angle_3_deg 13.042 r_dihedral_angle_1_deg 6.795 r_lrange_it 6.254 r_lrange_other 6.254 r_scangle_it 4.831 r_scangle_other 4.831 r_scbond_it 3.225 r_scbond_other 3.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.522 r_dihedral_angle_2_deg 13.823 r_dihedral_angle_3_deg 13.042 r_dihedral_angle_1_deg 6.795 r_lrange_it 6.254 r_lrange_other 6.254 r_scangle_it 4.831 r_scangle_other 4.831 r_scbond_it 3.225 r_scbond_other 3.224 r_mcangle_it 3.124 r_mcangle_other 3.124 r_mcbond_it 2.247 r_mcbond_other 2.246 r_angle_refined_deg 1.633 r_angle_other_deg 0.571 r_nbd_refined 0.254 r_symmetry_xyhbond_nbd_refined 0.229 r_nbd_other 0.198 r_symmetry_nbd_other 0.19 r_symmetry_nbd_refined 0.186 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.162 r_metal_ion_refined 0.154 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_chiral_restr_other 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5573 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing