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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 9 0.1 M PCB (SODIUM PROPIONATE, SODIUM CACODYLATE, BIS-TRIS PROPANE, 2:1:2) BUFFER PH 9.0 25% (W/V) PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.2 50.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.07 α = 83.09 b = 63.09 β = 76.9 c = 67.16 γ = 79.21
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 PILATUS 6M 2013-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 2.1 47.59 96.3 0.09 7.7 2.1 51094 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 2.1 2.16 95.4 0.81 1.7 2.1
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 PDB ENTRY 3ZKW 2.1 65.19 48582 2510 96.25 0.22039 0.21831 0.223 0.26021 0.2601 RANDOM 31.158
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] -1.45 -1.33 0.8 -0.28 1.82 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.738 r_dihedral_angle_3_deg 16.758 r_dihedral_angle_4_deg 13.184 r_long_range_B_refined 6.19 r_long_range_B_other 6.19 r_dihedral_angle_1_deg 6.034 r_scangle_other 4.457 r_mcangle_it 3.596 r_mcangle_other 3.596 r_scbond_it 2.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.738 r_dihedral_angle_3_deg 16.758 r_dihedral_angle_4_deg 13.184 r_long_range_B_refined 6.19 r_long_range_B_other 6.19 r_dihedral_angle_1_deg 6.034 r_scangle_other 4.457 r_mcangle_it 3.596 r_mcangle_other 3.596 r_scbond_it 2.872 r_scbond_other 2.872 r_mcbond_it 2.406 r_mcbond_other 2.405 r_angle_refined_deg 1.656 r_angle_other_deg 1.298 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 6598 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement xia2 data reduction