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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 2.16 42.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.15 α = 90 b = 66.31 β = 90.75 c = 63.52 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 PILATUS3 6M 2020-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
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 2.07 45.87 99.7 0.121 7.43 3.47 18557
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 2.07 2.12 0.599 1.93
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3UHM 2.07 45.87 17614 927 99.96 0.16881 0.16623 0.1752 0.21542 0.2177 RANDOM 28.197
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] -1.36 -0.42 -0.24 1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.725 r_dihedral_angle_3_deg 14.464 r_dihedral_angle_4_deg 13.678 r_long_range_B_refined 7.634 r_long_range_B_other 7.591 r_dihedral_angle_1_deg 6.342 r_scangle_other 5.33 r_scbond_it 3.492 r_scbond_other 3.49 r_mcangle_it 3.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.725 r_dihedral_angle_3_deg 14.464 r_dihedral_angle_4_deg 13.678 r_long_range_B_refined 7.634 r_long_range_B_other 7.591 r_dihedral_angle_1_deg 6.342 r_scangle_other 5.33 r_scbond_it 3.492 r_scbond_other 3.49 r_mcangle_it 3.049 r_mcangle_other 3.049 r_mcbond_it 2.173 r_mcbond_other 2.172 r_angle_refined_deg 1.78 r_angle_other_deg 1.112 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 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 182 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing