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Crystal structure of Danio rerio HDAC6 CD2 in complex with in situ enzymatically hydrolyzed DFMO-based ITF5924
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1 M Na-citrate pH 6.5, 20% (v/v) PEG4000, 20% (v/v) isopropanol
Crystal Properties Matthews coefficient Solvent content 2.36 47.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.372 α = 90 b = 118.924 β = 93.87 c = 60.263 γ = 90
Symmetry Space Group P 1 21 1
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 2021-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.283 ELETTRA 11.2C
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 1.6 47.88 95.6 0.133 0.143 0.052 0.998 8.8 7.5 92341 19.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 91.9 2.494 2.683 1.356 0.37 0.8 7.4
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 MOLECULAR REPLACEMENT THROUGHOUT 5EEK 1.6 47.88 87601 4695 95.42 0.1568 0.155 0.1695 0.1903 0.1989 RANDOM 23.673
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] -0.19 -0.81 1.03 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.953 r_dihedral_angle_4_deg 16.361 r_dihedral_angle_3_deg 12.912 r_dihedral_angle_1_deg 6.408 r_angle_refined_deg 1.609 r_angle_other_deg 1.479 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.953 r_dihedral_angle_4_deg 16.361 r_dihedral_angle_3_deg 12.912 r_dihedral_angle_1_deg 6.408 r_angle_refined_deg 1.609 r_angle_other_deg 1.479 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5580 Nucleic Acid Atoms Solvent Atoms 686 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing