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Crystal structure of the ferric enterobactin receptor mutant R480A from Pseudomonas aeruginosa (PfeA) in complex with enterobactin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 294 PEG 8000 ADA Magnesium acetate
Crystal Properties Matthews coefficient Solvent content 3.48 64.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.5 α = 90 b = 157.26 β = 90 c = 78 γ = 90
Symmetry Space Group P 21 21 2
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 2019-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96860 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 3.11 43.51 100 0.087 0.999 14.2 7.5 19766
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 3.11 3.16 100 0.52 1.1 8.8
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 6Q5E 3.11 43.51 18734 996 99.76 0.21413 0.21189 0.2109 0.25644 0.2455 RANDOM 126.632
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] 8.67 -2.39 -6.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.314 r_dihedral_angle_3_deg 17.237 r_dihedral_angle_4_deg 16.908 r_long_range_B_refined 10.856 r_long_range_B_other 10.855 r_dihedral_angle_1_deg 9.405 r_scangle_other 8.968 r_mcangle_it 7.962 r_mcangle_other 7.961 r_scbond_it 5.979
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.314 r_dihedral_angle_3_deg 17.237 r_dihedral_angle_4_deg 16.908 r_long_range_B_refined 10.856 r_long_range_B_other 10.855 r_dihedral_angle_1_deg 9.405 r_scangle_other 8.968 r_mcangle_it 7.962 r_mcangle_other 7.961 r_scbond_it 5.979 r_scbond_other 5.979 r_mcbond_it 5.439 r_mcbond_other 5.439 r_angle_refined_deg 1.322 r_angle_other_deg 1.157 r_chiral_restr 0.052 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 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 5364 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction DIALS data scaling PHASER phasing