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Crystal structure of LpxC from Pseudomonas aeruginosa in complex with PT801
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UPG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 100mM HEPES HCl, pH 7.5, 50mM CaCl2, 4% (w/v) Propanol, 25% (w/v) PEG 3350, PsaeA.00166.a.DG15.PD00442 at 5mg/ml + 1mM ZnCl2 + 1mM BSI 108451, Cryo = 20%EG: tray 298107e10
Crystal Properties Matthews coefficient Solvent content 2.07 40.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.71 α = 111.32 b = 48 β = 108.56 c = 48.13 γ = 98.83
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 mirrors 2018-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.55 42.585 96.4 0.077 0.089 0.997 11.3 3.952 37740 12.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.59 94.4 0.507 0.586 0.844 2.69 3.986
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 5UPG 1.55 42.585 1.98 37735 2034 96.77 0.1517 0.1496 0.151 0.1884 0.1899
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 19.31 f_angle_d 0.838 f_chiral_restr 0.056 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2331 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 76
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction Coot model building PHENIX phasing