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Crystal Structure of Deacetylase (HdaH) from Klebsiella pneumoniae subsp. ozaenae in complex with the inhibitor SAHA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G0X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 2% (w/v) PEG 8000, 10% (v/v) glycerol and 0.5M KCl
Crystal Properties Matthews coefficient Solvent content 3.13 60.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.206 α = 90 b = 146.206 β = 90 c = 146.206 γ = 90
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 16M mirror 2019-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.000000 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.95 46.3 100 0.02 0.028 0.02 1 16.3 1.9 37885 -3 41.09
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 100 0.844 0.597 0.532 1.3 2
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 1.95 46.277 37871 1859 99.989 0.139 0.1373 0.1387 0.1756 0.1784 48.525
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.891 r_dihedral_angle_3_deg 13.017 r_dihedral_angle_2_deg 9.305 r_lrange_it 8.753 r_lrange_other 8.639 r_dihedral_angle_1_deg 6.455 r_scangle_it 6.383 r_scangle_other 6.382 r_scbond_it 4.598 r_scbond_other 4.596
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.891 r_dihedral_angle_3_deg 13.017 r_dihedral_angle_2_deg 9.305 r_lrange_it 8.753 r_lrange_other 8.639 r_dihedral_angle_1_deg 6.455 r_scangle_it 6.383 r_scangle_other 6.382 r_scbond_it 4.598 r_scbond_other 4.596 r_mcangle_it 4.457 r_mcangle_other 4.456 r_mcbond_it 3.392 r_mcbond_other 3.39 r_angle_refined_deg 1.962 r_angle_other_deg 0.647 r_metal_ion_refined 0.254 r_xyhbond_nbd_refined 0.239 r_nbd_refined 0.238 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.185 r_nbd_other 0.145 r_symmetry_nbd_refined 0.12 r_symmetry_xyhbond_nbd_refined 0.107 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.036 r_bond_refined_d 0.012 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 2822 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing