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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 2.43 49.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.367 α = 90 b = 51.18 β = 108.22 c = 96.763 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 IMAGE PLATE RIGAKU RAXIS VII 2016-04-23 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 23.31 96.9 0.077 13.7 7.47 41967
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 2.07 94.4 0.313 5.6 7.32
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 23.32 39816 2150 96.83 0.1896 0.18685 0.193 0.24088 0.2441 RANDOM 32.92
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] -0.02 -0.02 0.07 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.738 r_dihedral_angle_4_deg 16.759 r_dihedral_angle_3_deg 16.141 r_dihedral_angle_1_deg 7.742 r_long_range_B_refined 7.486 r_long_range_B_other 7.471 r_scangle_other 5.656 r_mcangle_it 4.083 r_mcangle_other 4.082 r_scbond_it 3.619
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.738 r_dihedral_angle_4_deg 16.759 r_dihedral_angle_3_deg 16.141 r_dihedral_angle_1_deg 7.742 r_long_range_B_refined 7.486 r_long_range_B_other 7.471 r_scangle_other 5.656 r_mcangle_it 4.083 r_mcangle_other 4.082 r_scbond_it 3.619 r_scbond_other 3.614 r_mcbond_it 2.773 r_mcbond_other 2.77 r_angle_refined_deg 1.601 r_angle_other_deg 1.323 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 4642 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling MOLREP phasing