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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 2.1 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.854 α = 90 b = 66.306 β = 90.63 c = 63.542 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 2017-07-12 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 1.9 63.54 99.1 0.154 9.4 5 23367
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 1.9 1.97 0.438
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 1.9 63.54 22135 1173 98.94 0.19617 0.19402 0.2022 0.238 0.2437 RANDOM 21.396
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] -0.3 0.29 -1.22 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.376 r_dihedral_angle_3_deg 14.411 r_dihedral_angle_4_deg 13.583 r_long_range_B_refined 7.025 r_long_range_B_other 6.943 r_dihedral_angle_1_deg 6.801 r_scangle_other 3.914 r_mcangle_other 2.806 r_mcangle_it 2.804 r_scbond_it 2.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.376 r_dihedral_angle_3_deg 14.411 r_dihedral_angle_4_deg 13.583 r_long_range_B_refined 7.025 r_long_range_B_other 6.943 r_dihedral_angle_1_deg 6.801 r_scangle_other 3.914 r_mcangle_other 2.806 r_mcangle_it 2.804 r_scbond_it 2.518 r_scbond_other 2.517 r_angle_refined_deg 1.949 r_mcbond_it 1.868 r_mcbond_other 1.86 r_angle_other_deg 1.093 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 2301 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing