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Structure of P. aeruginosa LpxC with compound 10: (2RS)-4-(5-(2-Fluoro-4-methoxyphenyl)-1-oxoisoindolin-2-yl)-N-hydroxy-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 26-30% (w/v) PEG 4000, 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.279 α = 90 b = 66.503 β = 90.76 c = 63.452 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 2015-06-01 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 1.9 45.906 91.1 0.095 0.994 6.6 1.86 42579 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2.01 0.732 0.405
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 1.9 45.906 23703 1185 99.317 0.206 0.2032 0.2081 0.2579 0.2574 27.44
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] 1.137 0.552 -0.413 -0.738
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.839 r_dihedral_angle_4_deg 16.998 r_dihedral_angle_1_deg 16.748 r_dihedral_angle_3_deg 14.872 r_lrange_it 5.71 r_lrange_other 5.609 r_scangle_it 3.568 r_scangle_other 3.567 r_mcangle_other 3.277 r_mcangle_it 3.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.839 r_dihedral_angle_4_deg 16.998 r_dihedral_angle_1_deg 16.748 r_dihedral_angle_3_deg 14.872 r_lrange_it 5.71 r_lrange_other 5.609 r_scangle_it 3.568 r_scangle_other 3.567 r_mcangle_other 3.277 r_mcangle_it 3.274 r_scbond_it 2.265 r_scbond_other 2.264 r_mcbond_it 2.065 r_mcbond_other 2.065 r_angle_refined_deg 1.637 r_angle_other_deg 1.317 r_symmetry_nbd_refined 0.27 r_nbd_refined 0.192 r_nbd_other 0.182 r_symmetry_nbd_other 0.18 r_xyhbond_nbd_refined 0.165 r_nbtor_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.137 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2286 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing