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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 7.5 293 0.02M 1,6-Hexanediol
0.02M 1-Butanol
0.02M 1,2-Propanediol
0.02M 2-Propanol
0.02M 1,4-Butanediol
0.02M 1,3-Propanediol
0.1M Sodium HEPES - MOPS pH 7.5
20 % v/v PEG 500 MME
10 % w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.35 47.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.311 α = 76.73 b = 50.47 β = 76.94 c = 145.857 γ = 60.85
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS VII 2016-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54184
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 2.5 22.78 96.4 0.113 6.9 3.28 40242
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 2.5 2.59 94.6 0.347 3 3.21
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3UHM 2.5 22.78 38331 1910 96.25 0.21393 0.21063 0.28254 0.281 RANDOM 38.279
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] -0.03 -0.01 0.03 0.02 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.601 r_dihedral_angle_3_deg 18.582 r_dihedral_angle_4_deg 16.877 r_long_range_B_refined 7.975 r_long_range_B_other 7.974 r_dihedral_angle_1_deg 6.693 r_scangle_other 4.105 r_mcangle_it 3.808 r_mcangle_other 3.807 r_scbond_it 2.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.601 r_dihedral_angle_3_deg 18.582 r_dihedral_angle_4_deg 16.877 r_long_range_B_refined 7.975 r_long_range_B_other 7.974 r_dihedral_angle_1_deg 6.693 r_scangle_other 4.105 r_mcangle_it 3.808 r_mcangle_other 3.807 r_scbond_it 2.486 r_scbond_other 2.486 r_mcbond_it 2.329 r_mcbond_other 2.327 r_angle_refined_deg 1.536 r_angle_other_deg 1.405 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 8968 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling MOLREP phasing