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Crystal structure of the Klebsiella pneumoniae LpxH / JH-LPH-107 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 0.91 mg/mL of LpxH,
0.1 mM LPH-107,
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 4.5,
and 16 % v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 2.94 58.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.16 α = 90 b = 106.16 β = 90 c = 53.55 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 PILATUS3 2M 2024-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.976480 ALS 5.0.3
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 46.27 99.93 0.999 16.52 10.2 23763 26.68
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 2.072 99.96 0.858 3.09 10.6
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 46.27 1.36 23762 1189 99.95 0.1949 0.1941 0.1948 0.2096 0.2105 31.87
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 13.0937 f_angle_d 0.5696 f_chiral_restr 0.0419 f_plane_restr 0.0036 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1901 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing