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Crystal structure of the ferric enterobactin receptor from Pseudomonas aeruginosa (PfeA) in complex with enterobactin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M9B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 294 PEG 8000 ADA Magnesium acetate
Crystal Properties Matthews coefficient Solvent content 3.41 63.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.63 α = 90 b = 159.26 β = 90 c = 78.61 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 PILATUS 2M 2015-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.7 85.63 99.9 0.057 22 6.5 30261
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 100 0.603 3 6.6
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 5m9b 2.7 79.63 28689 1531 99.92 0.21002 0.2079 0.2102 0.24938 0.2491 RANDOM 74.148
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] 1.98 3.35 -5.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.186 r_dihedral_angle_4_deg 17.509 r_dihedral_angle_3_deg 16.69 r_dihedral_angle_1_deg 8.575 r_long_range_B_refined 7.219 r_long_range_B_other 7.219 r_scangle_other 5.761 r_mcangle_it 4.769 r_mcangle_other 4.769 r_scbond_it 4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.186 r_dihedral_angle_4_deg 17.509 r_dihedral_angle_3_deg 16.69 r_dihedral_angle_1_deg 8.575 r_long_range_B_refined 7.219 r_long_range_B_other 7.219 r_scangle_other 5.761 r_mcangle_it 4.769 r_mcangle_other 4.769 r_scbond_it 4 r_scbond_other 4 r_mcbond_it 3.348 r_mcbond_other 3.347 r_angle_refined_deg 1.416 r_angle_other_deg 1.22 r_chiral_restr 0.051 r_gen_planes_refined 0.016 r_bond_refined_d 0.007 r_gen_planes_other 0.004 r_bond_other_d 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 5370 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing