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Crystal structure of the ferric enterobactin receptor (PfeA) in complex with protochelin from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M9K
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 3.39 63.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.751 α = 90 b = 157.352 β = 90 c = 78.108 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 6M 2016-04-28 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 2.8 157.35 100 0.054 0.999 19.5 7.2 26955
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 2.8 2.813 97.6 0.695 0.867 2.3 7.7
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 5M9K 2.8 78.68 25602 1310 99.93 0.22026 0.21811 0.2169 0.26326 0.2531 RANDOM 110.265
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] 2.46 2.15 -4.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.952 r_dihedral_angle_3_deg 17.1 r_dihedral_angle_4_deg 16.549 r_long_range_B_refined 11.031 r_long_range_B_other 11.031 r_dihedral_angle_1_deg 9.506 r_scangle_other 8.398 r_mcangle_it 7.583 r_mcangle_other 7.536 r_scbond_it 6.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.952 r_dihedral_angle_3_deg 17.1 r_dihedral_angle_4_deg 16.549 r_long_range_B_refined 11.031 r_long_range_B_other 11.031 r_dihedral_angle_1_deg 9.506 r_scangle_other 8.398 r_mcangle_it 7.583 r_mcangle_other 7.536 r_scbond_it 6.095 r_scbond_other 6.094 r_mcbond_it 5.596 r_mcbond_other 5.571 r_angle_refined_deg 1.406 r_angle_other_deg 0.708 r_chiral_restr 0.097 r_gen_planes_refined 0.015 r_bond_refined_d 0.012 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 5363 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing