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Crystal structure of LpxC from Pseudomonas aeruginosa in complex with racemic ligand PT803
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VWM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 290 tray296747a A10: 100 mM Tris-HCl, pH 8.5, 30% (w/v) Propanol, 30% (w/v) PEG 3350 +1mM ZnCl2, 1mM BSI108453 (PT803) : Cryo = 20%EG
: PsaeA.00166.a.DG15.PD00471 at 5 mg/ml, puck qcu4-1
Crystal Properties Matthews coefficient Solvent content 2.24 45.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.66 α = 90 b = 79.34 β = 92.01 c = 50.92 γ = 90
Symmetry Space Group P 1 21 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 CCD RAYONIX MX-300 mirrors 2017-12-07 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 2 35.638 97.1 0.098 0.113 0.997 11.72 4.114 18652 21.34
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 2 2.05 76.8 0.563 0.662 0.769 2.02 3.387
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 THROUGHOUT 5VWM 2 35.638 1.35 18648 1907 97.05 0.1675 0.1623 0.164 0.2134 0.2147
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 19.81 f_angle_d 1.14 f_chiral_restr 0.127 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2249 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 93
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction MOLREP phasing