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Structure of P. aeruginosa LpxC with compound 18d: (2R)-N-Hydroxy-4-(6-((1-(hydroxymethyl)cyclopropyl)buta-1,3-diyn-1-yl)-3-oxo-1H-pyrrolo[1,2-c]imidazol-2(3H)-yl)-2-methyl-2-(methylsulfonyl)butanamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VES
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M trimethylamine N-oxide, 0.1 M Tris pH 8.5, 20 % PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.29 46.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.071 α = 90 b = 66.485 β = 90.648 c = 63.193 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 PILATUS 2M-F 2017-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.25 36.003 99.7 0.993 4.8 3.45 14233
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.39 99.3 1.25 0.46 1.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2ves 2.251 36.003 14226 709 99.587 0.228 0.225 0.2257 0.2812 0.2826 27.39
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] -0.019 -0.473 -1.512 1.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.152 r_dihedral_angle_1_deg 15.677 r_dihedral_angle_3_deg 14.571 r_dihedral_angle_4_deg 14.551 r_lrange_it 3.661 r_lrange_other 3.594 r_angle_refined_deg 1.986 r_mcangle_it 1.973 r_mcangle_other 1.973 r_scangle_it 1.857
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.152 r_dihedral_angle_1_deg 15.677 r_dihedral_angle_3_deg 14.571 r_dihedral_angle_4_deg 14.551 r_lrange_it 3.661 r_lrange_other 3.594 r_angle_refined_deg 1.986 r_mcangle_it 1.973 r_mcangle_other 1.973 r_scangle_it 1.857 r_scangle_other 1.856 r_angle_other_deg 1.303 r_mcbond_it 1.133 r_mcbond_other 1.133 r_scbond_it 1.072 r_scbond_other 1.071 r_symmetry_nbd_refined 0.268 r_nbd_refined 0.175 r_symmetry_nbd_other 0.175 r_nbd_other 0.173 r_symmetry_xyhbond_nbd_refined 0.152 r_nbtor_refined 0.15 r_xyhbond_nbd_refined 0.141 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2287 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing