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Crystal structure of Klebsiella LpxH in complex with JH-LPH-50
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 4 mg/mL of LpxH,
0.27 mM JH-LPH-50,
10 mM MES (pH 6.0),
100 mM NaCl,
0.5 mM DTT,
2.5% glycerol,
0.625% DMSO,
0.05 M calcium chloride dihydrate,
0.05 M Tris pH 6.5,
6.5 % w/v PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.96 58.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.53 α = 90 b = 106.53 β = 90 c = 53.56 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 2019-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
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 1.73 46.32 99.94 0.999 21.98 11.6 36774 21.65
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 1.73 1.792 0.929
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6PJ3 1.73 46.32 1.37 36765 1839 99.95 0.1693 0.1681 0.1678 0.1931 0.1938 28.24
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 17.2964 f_angle_d 0.8813 f_chiral_restr 0.0623 f_plane_restr 0.0077 f_bond_d 0.0074
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1872 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 65
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing