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Crystal Structure of Histone deacetylase (HdaH) from Vibrio cholerae in complex with decanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A395TF31-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 1 M Na/K tartrate,
0.1 M imidazole pH 8
0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 1.94 36.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.11 α = 90 b = 51.15 β = 102.22 c = 108.82 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 PILATUS3 S 2M 2021-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918400 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 1.13 50 94.7 0.07 0.083 0.999 8.16 3.45 194694 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.13 1.2 90 1.672 1.997 0.301 0.65 3.25
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.13 46.139 194690 9727 94.706 0.159 0.1575 0.1788 0.1662 17.375
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] -0.184 -0.325 0.252 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.294 r_dihedral_angle_3_deg 11.153 r_dihedral_angle_2_deg 8.367 r_dihedral_angle_1_deg 6.001 r_lrange_it 5.973 r_lrange_other 5.631 r_scangle_it 3.305 r_scangle_other 3.305 r_scbond_it 2.226 r_scbond_other 2.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.294 r_dihedral_angle_3_deg 11.153 r_dihedral_angle_2_deg 8.367 r_dihedral_angle_1_deg 6.001 r_lrange_it 5.973 r_lrange_other 5.631 r_scangle_it 3.305 r_scangle_other 3.305 r_scbond_it 2.226 r_scbond_other 2.226 r_angle_refined_deg 1.962 r_mcangle_other 1.927 r_mcangle_it 1.926 r_mcbond_it 1.276 r_mcbond_other 1.266 r_angle_other_deg 0.689 r_symmetry_xyhbond_nbd_refined 0.466 r_nbd_refined 0.277 r_symmetry_nbd_refined 0.25 r_xyhbond_nbd_refined 0.224 r_xyhbond_nbd_other 0.219 r_metal_ion_refined 0.206 r_symmetry_nbd_other 0.197 r_symmetry_metal_ion_refined 0.19 r_nbtor_refined 0.183 r_nbd_other 0.153 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.069 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4838 Nucleic Acid Atoms Solvent Atoms 791 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing