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The Periplasmic Binding Protein CeuE of Campylobacter jejuni preferentially binds the iron(III) complex of the Linear Dimer Component of Enterobactin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZKW PDB ENTRY 3ZKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.1 M MMT (DL-MALIC ACID, MES, TRIS, 1:2:2) BUFFER, PH 8.0, 25% (W/V) PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.461 α = 83.36 b = 63.021 β = 76.57 c = 67.011 γ = 78.24
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 2014-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.9 45.76 98.1 0.1 17.5 4.4 70279 2
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 1.9 1.94 96.1 0.9 2.2 4.2
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 PDB ENTRY 3ZKW 1.9 65.01 66562 3495 97.78 0.22676 0.2248 0.231 0.26407 0.2671 RANDOM 42.232
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] -1.58 -1.62 0.39 -1.11 0.99 2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.449 r_dihedral_angle_4_deg 18.855 r_dihedral_angle_3_deg 16.108 r_long_range_B_refined 8.083 r_long_range_B_other 8.082 r_dihedral_angle_1_deg 6.583 r_scangle_other 6.304 r_mcangle_it 5.315 r_mcangle_other 5.314 r_scbond_it 4.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.449 r_dihedral_angle_4_deg 18.855 r_dihedral_angle_3_deg 16.108 r_long_range_B_refined 8.083 r_long_range_B_other 8.082 r_dihedral_angle_1_deg 6.583 r_scangle_other 6.304 r_mcangle_it 5.315 r_mcangle_other 5.314 r_scbond_it 4.415 r_scbond_other 4.414 r_mcbond_it 3.954 r_mcbond_other 3.954 r_angle_refined_deg 1.775 r_angle_other_deg 1.39 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.008 r_gen_planes_other 0.007 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 6581 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement xia2 data reduction