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Crystal structure of the ferric enterobactin esterase (pfeE) mutant(S157A) from Pseudomonas aeruginosa in complex with Tris-catechol vector
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GI0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 294 PEG MME 2000, Sodium acetate, potassium nitrate
Crystal Properties Matthews coefficient Solvent content 2.35 47.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.794 α = 90 b = 76.602 β = 90 c = 129.867 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 S 6M 2017-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.48 129.87 100 0.058 0.999 16.8 7.2 95776
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 1.48 1.51 99.3 0.796 0.863 2.2 7.1
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 6GI0 1.49 65.98 90838 4849 99.92 0.17439 0.17312 0.1805 0.19895 0.2052 RANDOM 26.077
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] 1.76 -0.16 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.335 r_dihedral_angle_4_deg 18.664 r_dihedral_angle_3_deg 13.09 r_long_range_B_refined 7.75 r_long_range_B_other 7.75 r_dihedral_angle_1_deg 6.505 r_scangle_other 6.409 r_scbond_it 4.278 r_scbond_other 4.277 r_mcangle_it 4.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.335 r_dihedral_angle_4_deg 18.664 r_dihedral_angle_3_deg 13.09 r_long_range_B_refined 7.75 r_long_range_B_other 7.75 r_dihedral_angle_1_deg 6.505 r_scangle_other 6.409 r_scbond_it 4.278 r_scbond_other 4.277 r_mcangle_it 4.039 r_mcangle_other 4.038 r_mcbond_it 2.899 r_mcbond_other 2.898 r_angle_refined_deg 1.423 r_angle_other_deg 0.754 r_chiral_restr 0.092 r_gen_planes_refined 0.014 r_bond_refined_d 0.013 r_gen_planes_other 0.002 r_bond_other_d 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 4010 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing