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Crystal Structure of Deacetylase (HdaH) from Klebsiella pneumoniae subsp. ozaenae in Complex with the inhibitor TSA
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 12% (w/v) PEG 8000, 10% (v/v) glycerol and 0.5M KCl
Crystal Properties Matthews coefficient Solvent content 3.16 61.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.57 α = 90 b = 146.57 β = 90 c = 146.57 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 2019-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.18 47 100 0.997 10.8 1.7 27454 -3 39.05
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 2.18 2.25 99.9 0.832 2.5
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 2.18 46.393 27437 1378 99.978 0.15 0.1478 0.1918 0.1862 0.235 43.205
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 16.486 r_dihedral_angle_3_deg 14.005 r_dihedral_angle_2_deg 11.793 r_lrange_other 10.202 r_lrange_it 10.172 r_scangle_it 9.272 r_scangle_other 9.27 r_scbond_it 7.262 r_scbond_other 7.262 r_dihedral_angle_1_deg 6.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.486 r_dihedral_angle_3_deg 14.005 r_dihedral_angle_2_deg 11.793 r_lrange_other 10.202 r_lrange_it 10.172 r_scangle_it 9.272 r_scangle_other 9.27 r_scbond_it 7.262 r_scbond_other 7.262 r_dihedral_angle_1_deg 6.855 r_mcangle_it 6.392 r_mcangle_other 6.392 r_mcbond_it 4.944 r_mcbond_other 4.943 r_angle_refined_deg 2.236 r_angle_other_deg 0.756 r_nbd_refined 0.246 r_metal_ion_refined 0.21 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.183 r_nbd_other 0.139 r_symmetry_nbd_refined 0.113 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_refined 0.056 r_symmetry_xyhbond_nbd_other 0.039 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 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 119 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction XDS data scaling PHASER phasing