☰ Navigation Tabs
LpxC Inhibitors With Fluoroproline As A Novel Zinc-Binding Group Can Serve As A Novel Class of Antibiotic With Activity Against Multidrug-Resistant Gram-Negative Bacteria
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, HANGING DROP 7 293 0.2 M NA ACETATE, 28% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.13 42.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.531 α = 90 b = 66.81 β = 90.35 c = 62.691 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 6M-F 2019-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 2.1 45.76 98.4 0.992 4.1 3.4 16931
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 2.1 2.16 0.651
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 2VES 2.1 45.76 15967 928 98.19 0.1822 0.1789 0.1879 0.23897 0.2473 RANDOM 31.432
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] -0.78 -0.03 -2.28 3.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.864 r_dihedral_angle_4_deg 19.568 r_dihedral_angle_3_deg 15.76 r_dihedral_angle_1_deg 7.409 r_long_range_B_refined 7.36 r_long_range_B_other 7.21 r_scangle_other 4.923 r_mcangle_it 3.52 r_mcangle_other 3.52 r_scbond_it 3.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.864 r_dihedral_angle_4_deg 19.568 r_dihedral_angle_3_deg 15.76 r_dihedral_angle_1_deg 7.409 r_long_range_B_refined 7.36 r_long_range_B_other 7.21 r_scangle_other 4.923 r_mcangle_it 3.52 r_mcangle_other 3.52 r_scbond_it 3.185 r_scbond_other 3.184 r_mcbond_it 2.312 r_mcbond_other 2.309 r_angle_refined_deg 1.558 r_angle_other_deg 1.34 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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 2286 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing