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Structure of P. aeruginosa LpxC with compound 17a: (2R)-N-Hydroxy-2-methyl-2-(methylsulfonyl)-4(6((4(morpholinomethyl)phenyl)ethynyl)-3-oxo-1H-pyrrolo[1,2-c]imidazol-2(3H)yl)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 ammonium acetate, 0.1 M sodium acetate pH 4.6, 7 % (w/v) PEG 400, 7 % (w/v) PEG 500 MME, 7 % (w/v) PEG 600, 7 % (w/v) PEG 1000, 5 % (v/v) ethylene glycol
Crystal Properties Matthews coefficient Solvent content 1.99 38.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.313 α = 90 b = 89.178 β = 90 c = 35.383 γ = 90
Symmetry Space Group P 21 21 2
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 2017-10-01 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) R Merge I (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 1.94 43.122 97.9 0.109 0.995 8.7 3.62 74154 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.06 96.4 0.725 2.1
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 1.94 43.122 39617 1982 98.186 0.186 0.1832 0.1835 0.2429 0.2424 24.151
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] 0.851 0.025 -0.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.557 r_dihedral_angle_4_deg 20.678 r_dihedral_angle_3_deg 14.384 r_dihedral_angle_1_deg 7.417 r_lrange_other 6.898 r_lrange_it 6.869 r_scangle_it 6.115 r_scangle_other 6.114 r_scbond_it 4.418 r_scbond_other 4.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.557 r_dihedral_angle_4_deg 20.678 r_dihedral_angle_3_deg 14.384 r_dihedral_angle_1_deg 7.417 r_lrange_other 6.898 r_lrange_it 6.869 r_scangle_it 6.115 r_scangle_other 6.114 r_scbond_it 4.418 r_scbond_other 4.417 r_mcangle_it 3.93 r_mcangle_other 3.929 r_mcbond_it 3.185 r_mcbond_other 3.171 r_angle_refined_deg 2.417 r_angle_other_deg 1.619 r_symmetry_nbd_refined 0.276 r_nbd_other 0.23 r_nbd_refined 0.219 r_symmetry_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.147 r_ncsr_local_group_1 0.12 r_chiral_restr 0.111 r_symmetry_nbtor_other 0.092 r_symmetry_xyhbond_nbd_other 0.065 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 r_xyhbond_nbd_other 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4545 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing