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Crystal structure of inactive Deacetylase (HdaH) H144A from Klebsiella pneumoniae subsp. ozaenae
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 3.13 60.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.117 α = 90 b = 146.117 β = 90 c = 146.117 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 PILATUS3 S 2M mirror 2019-03-15 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 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 2.35 46.54 100 0.116 0.119 0.027 0.999 20.8 20 22209 -3 43.14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 100 0.955 0.978 0.21 0.913 3.2 16.05
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 2.35 46.249 21754 1152 99.972 0.156 0.1533 0.1581 0.2042 0.2147 47.322
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 15.552 r_dihedral_angle_3_deg 14.893 r_dihedral_angle_2_deg 10.165 r_lrange_other 8.914 r_lrange_it 8.91 r_dihedral_angle_1_deg 7.7 r_scangle_it 7.392 r_scangle_other 7.302 r_mcangle_it 5.994 r_mcangle_other 5.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.552 r_dihedral_angle_3_deg 14.893 r_dihedral_angle_2_deg 10.165 r_lrange_other 8.914 r_lrange_it 8.91 r_dihedral_angle_1_deg 7.7 r_scangle_it 7.392 r_scangle_other 7.302 r_mcangle_it 5.994 r_mcangle_other 5.993 r_scbond_it 5.59 r_scbond_other 5.505 r_mcbond_it 4.591 r_mcbond_other 4.567 r_angle_refined_deg 2.304 r_angle_other_deg 0.729 r_nbd_refined 0.26 r_metal_ion_refined 0.235 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.174 r_nbd_other 0.167 r_chiral_restr 0.095 r_symmetry_nbd_refined 0.094 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_refined 0.046 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2817 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction XDS data scaling PHASER phasing