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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 7 293 20 % w/v Polyethylene glycol 6,000
100 mM HEPES pH 7.0
200 mM Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.45 49.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.475 α = 76.18 b = 50.772 β = 72.38 c = 76.063 γ = 61.57
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 2016-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.7 31.3 96.4 0.129 6.7 3.85 16646
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 2.7 2.8 95.8 0.468 1.9 3.93
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 2.7 31.32 15784 862 96.37 0.25677 0.25223 0.3366 0.3053 RANDOM 49.899
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] -0.09 -0.1 0.1 0.09 -0.01 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.654 r_dihedral_angle_3_deg 19.661 r_dihedral_angle_4_deg 14.281 r_long_range_B_refined 10.053 r_long_range_B_other 10.053 r_dihedral_angle_1_deg 6.701 r_mcangle_it 5.132 r_mcangle_other 5.132 r_scangle_other 4.836 r_mcbond_it 3.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.654 r_dihedral_angle_3_deg 19.661 r_dihedral_angle_4_deg 14.281 r_long_range_B_refined 10.053 r_long_range_B_other 10.053 r_dihedral_angle_1_deg 6.701 r_mcangle_it 5.132 r_mcangle_other 5.132 r_scangle_other 4.836 r_mcbond_it 3.213 r_mcbond_other 3.205 r_scbond_it 2.945 r_scbond_other 2.944 r_angle_refined_deg 1.432 r_angle_other_deg 1.307 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 4668 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling MOLREP phasing