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Crystal structure of the Klebsiella pneumoniae LpxH / JH-LPH-106 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 1.1 mg/mL of LpxH,
0.15 mM LPH-106,
10 mM MES (pH 6.0),
100 mM NaCl,
0.5 mM DTT,
2.5% glycerol,
0.8% DMSO,
0.05 M HEPES pH 6.5,
and 18 % w/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 PILATUS 6M 2024-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000040 ALS 5.0.2
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 1.72 45.97 98.96 0.981 6.99 9.9 36785 19.98
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 1.72 1.782 0.853
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 1.72 45.97 1.35 36771 1837 98.97 0.1826 0.181 0.1811 0.2123 0.2141 27.26
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 20.2586 f_angle_d 1.3574 f_chiral_restr 0.097 f_bond_d 0.0161 f_plane_restr 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1931 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing