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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 3350, 0.2 M NA FORMATE
Crystal Properties Matthews coefficient Solvent content 2.13 42.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.432 α = 90 b = 66.593 β = 91.24 c = 62.884 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 2019-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 62.87 98.3 0.99 4.2 3.4 19507
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 2.05 0.438 1.1
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 62.87 18454 1014 97.97 0.19687 0.19437 0.2038 0.24126 0.2474 RANDOM 33.234
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] 0.98 0.66 -3.64 2.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.248 r_dihedral_angle_4_deg 18.473 r_dihedral_angle_3_deg 16.081 r_long_range_B_refined 7.951 r_long_range_B_other 7.924 r_dihedral_angle_1_deg 6.997 r_scangle_other 5.649 r_scbond_it 3.582 r_scbond_other 3.58 r_mcangle_it 3.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.248 r_dihedral_angle_4_deg 18.473 r_dihedral_angle_3_deg 16.081 r_long_range_B_refined 7.951 r_long_range_B_other 7.924 r_dihedral_angle_1_deg 6.997 r_scangle_other 5.649 r_scbond_it 3.582 r_scbond_other 3.58 r_mcangle_it 3.52 r_mcangle_other 3.519 r_mcbond_it 2.379 r_mcbond_other 2.374 r_angle_refined_deg 1.643 r_angle_other_deg 1.384 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 2237 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing