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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-(pyrrolidin-1-yl)phenyl)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 M sodium formate, 22 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.711 α = 90 b = 87.033 β = 90 c = 178.864 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 2024-01-31 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 2.14 44.76 99.7 0.994 6.5 7.5 18936
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 2.14 2.2 0.203
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 (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 2.14 44.76 17948 947 99.67 0.2094 0.20751 0.2121 0.24722 0.251 RANDOM 41.061
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] -2.95 -1.8 4.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.789 r_dihedral_angle_1_deg 6.971 r_dihedral_angle_2_deg 6.914 r_long_range_B_refined 2.394 r_long_range_B_other 2.392 r_angle_refined_deg 1.01 r_mcangle_it 0.49 r_mcangle_other 0.49 r_scangle_other 0.437 r_angle_other_deg 0.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.789 r_dihedral_angle_1_deg 6.971 r_dihedral_angle_2_deg 6.914 r_long_range_B_refined 2.394 r_long_range_B_other 2.392 r_angle_refined_deg 1.01 r_mcangle_it 0.49 r_mcangle_other 0.49 r_scangle_other 0.437 r_angle_other_deg 0.393 r_mcbond_it 0.27 r_mcbond_other 0.27 r_scbond_it 0.243 r_scbond_other 0.243 r_chiral_restr 0.046 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2759 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 34
Software Software Software Name Purpose autoPROC data processing XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building