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Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) in complex with N-((6-(Hydroxyamino)-6-oxohexyl)oxy)-4-(4-methoxyphenyl)thiazole-2-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M sodium acetate, 0.1 sodium formate, 28% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.05 40.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.278 α = 90 b = 87.098 β = 90 c = 179.771 γ = 90
Symmetry Space Group C 2 2 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 4M 2024-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967700 ESRF MASSIF-3
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 1.9 44.983 94.6 0.995 9.4 7.5 25240
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 1.9 1.94 90.6 0.453 6.8
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 1.9 44.983 25189 1260 94.172 0.211 0.208 0.2007 0.2672 0.2592 27.23
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] 0.196 -0.852 0.656
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.394 r_dihedral_angle_3_deg 13.204 r_dihedral_angle_2_deg 10.945 r_dihedral_angle_1_deg 6.715 r_lrange_it 6.125 r_scangle_it 4.818 r_scbond_it 3.202 r_mcangle_it 3.092 r_mcbond_it 2.15 r_angle_refined_deg 1.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.394 r_dihedral_angle_3_deg 13.204 r_dihedral_angle_2_deg 10.945 r_dihedral_angle_1_deg 6.715 r_lrange_it 6.125 r_scangle_it 4.818 r_scbond_it 3.202 r_mcangle_it 3.092 r_mcbond_it 2.15 r_angle_refined_deg 1.876 r_nbtor_refined 0.314 r_nbd_refined 0.215 r_symmetry_nbd_refined 0.214 r_symmetry_xyhbond_nbd_refined 0.168 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.114 r_metal_ion_refined 0.043 r_gen_planes_refined 0.008 r_bond_refined_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2744 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 30
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing Coot model building REFMAC refinement