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Crystal structure of P.aeruginosa LpxC in complex with inhibitor
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 9.5 293 20 % w/v Polyethylene glycol 8,000, 100 mM CHES pH 9.5
Crystal Properties Matthews coefficient Solvent content 2.29 46.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.613 α = 90 b = 66.859 β = 90.42 c = 62.89 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 PIXEL DECTRIS PILATUS 200K 2016-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54056
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.15 62.89 99.8 0.16 11.59 5.2 16154
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 0.672 2.01
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3UHM 2.15 62.89 15359 747 99.65 0.19519 0.19195 0.1999 0.25628 0.2663 RANDOM 23.301
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] -0.13 0.47 -0.97 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.937 r_dihedral_angle_4_deg 17.582 r_dihedral_angle_3_deg 16.314 r_long_range_B_refined 7.485 r_long_range_B_other 7.446 r_dihedral_angle_1_deg 6.357 r_scangle_other 3.807 r_mcangle_other 2.899 r_mcangle_it 2.89 r_scbond_it 2.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.937 r_dihedral_angle_4_deg 17.582 r_dihedral_angle_3_deg 16.314 r_long_range_B_refined 7.485 r_long_range_B_other 7.446 r_dihedral_angle_1_deg 6.357 r_scangle_other 3.807 r_mcangle_other 2.899 r_mcangle_it 2.89 r_scbond_it 2.326 r_scbond_other 2.325 r_mcbond_it 1.819 r_angle_refined_deg 1.802 r_mcbond_other 1.797 r_angle_other_deg 1.022 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2295 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing