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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, SITTING DROP 8.5 292 0.1 M TRIS pH 8.5
30% Polyethylene glycol 4K
0.2M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.01 38.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.91 α = 90 b = 76.25 β = 90 c = 97.49 γ = 90
Symmetry Space Group P 21 21 21
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 2015-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
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 1.92 19.5 95 0.063 20.16 4.78 20142
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 1.92 1.97 48.2 0.548 2.64 2.41
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 1.92 19.5 19044 1050 95.04 0.16803 0.16544 0.1751 0.21331 0.2151 RANDOM 20.966
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] -0.68 0.16 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.787 r_dihedral_angle_4_deg 21.485 r_dihedral_angle_3_deg 14.271 r_dihedral_angle_1_deg 7.375 r_long_range_B_refined 6.088 r_long_range_B_other 6.014 r_scangle_other 4.483 r_scbond_it 2.876 r_scbond_other 2.875 r_mcangle_other 2.788
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.787 r_dihedral_angle_4_deg 21.485 r_dihedral_angle_3_deg 14.271 r_dihedral_angle_1_deg 7.375 r_long_range_B_refined 6.088 r_long_range_B_other 6.014 r_scangle_other 4.483 r_scbond_it 2.876 r_scbond_other 2.875 r_mcangle_other 2.788 r_mcangle_it 2.778 r_mcbond_it 1.859 r_mcbond_other 1.835 r_angle_refined_deg 1.626 r_angle_other_deg 1.367 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2324 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing