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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 2.16 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.432 α = 90 b = 67.039 β = 90.3 c = 63.336 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 2019-11-28 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 2.014 46.08 86.3 0.994 8.3 3.2 13479
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 2.014 2.177 0.592 1.7
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 2.01 46.08 12840 643 68.18 0.19569 0.19272 0.2005 0.25334 0.2477 RANDOM 28.795
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] 0.08 -0.13 0.36 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.554 r_dihedral_angle_4_deg 18.983 r_dihedral_angle_3_deg 17.338 r_dihedral_angle_1_deg 7.256 r_long_range_B_refined 5.098 r_long_range_B_other 5.066 r_scangle_other 3.63 r_mcangle_it 2.79 r_mcangle_other 2.79 r_scbond_it 2.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.554 r_dihedral_angle_4_deg 18.983 r_dihedral_angle_3_deg 17.338 r_dihedral_angle_1_deg 7.256 r_long_range_B_refined 5.098 r_long_range_B_other 5.066 r_scangle_other 3.63 r_mcangle_it 2.79 r_mcangle_other 2.79 r_scbond_it 2.288 r_scbond_other 2.287 r_mcbond_it 1.833 r_mcbond_other 1.833 r_angle_refined_deg 1.464 r_angle_other_deg 1.199 r_chiral_restr 0.058 r_bond_refined_d 0.006 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 2236 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing