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Crystal Structure of the Klebsiella pneumoniae LpxH/JH-LPH-86 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PJ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1 mg/mL of LpxH,
0.14 mM LPH-86,
10 mM MES (pH 6.0),
100 mM NaCl,
0.5 mM DTT,
2.5% glycerol,
0.8% DMSO,
0.05 M sodium acetate pH 5.0,
and 18 % v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 3.01 59.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.63 α = 90 b = 106.63 β = 90 c = 54.27 γ = 120
Symmetry Space Group P 32 2 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 EIGER X 16M 2023-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
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 2.3 46.79 99.15 0.998 13.56 8 15953 42.44
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 2.3 2.38 0.913
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 46.79 1.36 15931 796 99.16 0.1958 0.1941 0.1951 0.2289 0.2273 52.84
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 f_dihedral_angle_d 16.2742 f_angle_d 0.7086 f_chiral_restr 0.0521 f_plane_restr 0.0064 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1900 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing