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The crystal structure of zebrafish HDAC6 CD2 in complex with compound 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 50mM HEPES pH 7,5, 100 mM KCl, 1 mM TCEP, 5% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.08 40.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.659 α = 90 b = 92.163 β = 90 c = 97.249 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 CCD RIGAKU 2018-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.54178
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 1.98 97.25 98.1 0.987 10.6 6.6 46725
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 1.98 2.08 0.33
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 1.98 66.89 46151 2297 97.3 0.232 0.229 0.246 0.282 0.3019 RANDOM 16.18
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] 4.3182 -9.9824 5.6642
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.6 t_omega_torsion 3.32 t_angle_deg 1.1 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_chiral_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.6 t_omega_torsion 3.32 t_angle_deg 1.1 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5556 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 64
Software Software Software Name Purpose BUSTER refinement XDS data reduction STARANISO data scaling MOLREP phasing