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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 26% PEG 1500, 0.2 M NA ACETATE
Crystal Properties Matthews coefficient Solvent content 2.19 43.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.779 α = 90 b = 67.163 β = 90 c = 63.617 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 EIGER2 XE 16M 2019-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.39 46.23 100 0.966 3.4 3.4 12020
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 2.39 2.45 0.394 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 (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 2.39 46.23 11374 628 99.9 0.20323 0.2002 0.2064 0.25688 0.2581 RANDOM 30.818
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] 0.43 2.07 -2.14 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.053 r_dihedral_angle_4_deg 19.306 r_dihedral_angle_3_deg 16.547 r_dihedral_angle_1_deg 8.003 r_long_range_B_refined 6.053 r_long_range_B_other 6.053 r_scangle_other 4.574 r_mcangle_it 3.671 r_mcangle_other 3.67 r_scbond_it 2.837
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.053 r_dihedral_angle_4_deg 19.306 r_dihedral_angle_3_deg 16.547 r_dihedral_angle_1_deg 8.003 r_long_range_B_refined 6.053 r_long_range_B_other 6.053 r_scangle_other 4.574 r_mcangle_it 3.671 r_mcangle_other 3.67 r_scbond_it 2.837 r_scbond_other 2.836 r_mcbond_it 2.412 r_mcbond_other 2.404 r_angle_refined_deg 1.527 r_angle_other_deg 1.255 r_chiral_restr 0.066 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 2296 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing