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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 Morpheus HT-96 (MD1-47). Well A9
Crystal Properties Matthews coefficient Solvent content 2.41 48.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.09 α = 90 b = 51.89 β = 105.61 c = 146.62 γ = 90
Symmetry Space Group C 1 2 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 6M-F 2016-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 1.78 43.93 97.5 0.047 10.7 2.8 59205
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 1.78 1.83 97.7 0.613 1.4 2.8
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 1.78 43.93 56161 3043 97.42 0.19229 0.18964 0.199 0.2416 0.246 RANDOM 30.416
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] -0.6 0.11 1.46 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.336 r_dihedral_angle_4_deg 17.515 r_dihedral_angle_3_deg 15.184 r_long_range_B_refined 7.875 r_long_range_B_other 7.868 r_dihedral_angle_1_deg 7.131 r_scangle_other 6.025 r_mcangle_it 3.862 r_mcangle_other 3.862 r_scbond_it 3.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.336 r_dihedral_angle_4_deg 17.515 r_dihedral_angle_3_deg 15.184 r_long_range_B_refined 7.875 r_long_range_B_other 7.868 r_dihedral_angle_1_deg 7.131 r_scangle_other 6.025 r_mcangle_it 3.862 r_mcangle_other 3.862 r_scbond_it 3.86 r_scbond_other 3.859 r_mcbond_it 2.761 r_mcbond_other 2.761 r_angle_refined_deg 1.655 r_angle_other_deg 1.35 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 4406 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing