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Crystal structure of LpxC from Pseudomonas aeruginosa in complex with PF-5081090
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 100mM HEPES HCl, pH 7.7, 50mM CaCl2, 4% (w/v) Propanol, 25% (w/v) PEG 3350, PsaeA.00166.a.DG15.PD00471 at 5mg/ml + 1mM ZnCl2 + 1mM BSI 101565 (PF-5081090), cryo: 20% EG: tray 285924g10
Crystal Properties Matthews coefficient Solvent content 2.06 40.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.84 α = 111.27 b = 47.4 β = 109.12 c = 48.15 γ = 98.12
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 RIGAKU SATURN 944 2017-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
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 1.7 40.91 97.7 0.084 0.09 0.998 18.42 7.242 28780 -3 9.93
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 1.7 1.74 88.6 0.539 0.634 0.733 2.38 3.289
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 3uhm 1.7 40.91 1.99 28779 2043 98.18 0.15 0.1472 0.1477 0.1857 0.1862 13.3442
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 19.692 f_angle_d 0.868 f_chiral_restr 0.055 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 375 Heterogen Atoms 111
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling Coot model building PDB_EXTRACT data extraction XDS data reduction MOLREP phasing