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A complex of the synthetic siderophore analogue Fe(III)-6-LICAM with the CeuE periplasmic protein from Campylobacter jejuni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A1J PDB ENTRY 5A1J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 0.1 M PCB BUFFER, PH 7, 25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.19 43.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.37 α = 90 b = 66.08 β = 90 c = 68.96 γ = 90
Symmetry Space Group P 21 21 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 2015-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 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 2.04 44.96 100 0.26 9.6 7.9 18467 1.5
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 2.04 2.09 100 1.24 1.7 8.2
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 5A1J 2.04 44.97 17437 988 99.93 0.21618 0.21346 0.2186 0.26528 0.2653 RANDOM 23.378
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] 0.03 -0.05 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.345 r_dihedral_angle_3_deg 16.285 r_dihedral_angle_4_deg 15.938 r_dihedral_angle_1_deg 6.33 r_long_range_B_refined 4.166 r_long_range_B_other 4.123 r_scangle_other 3.058 r_mcangle_other 2.39 r_mcangle_it 2.388 r_scbond_it 1.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.345 r_dihedral_angle_3_deg 16.285 r_dihedral_angle_4_deg 15.938 r_dihedral_angle_1_deg 6.33 r_long_range_B_refined 4.166 r_long_range_B_other 4.123 r_scangle_other 3.058 r_mcangle_other 2.39 r_mcangle_it 2.388 r_scbond_it 1.959 r_scbond_other 1.958 r_angle_refined_deg 1.635 r_mcbond_it 1.594 r_mcbond_other 1.585 r_angle_other_deg 0.836 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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 2214 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement xia2 data reduction PHASER phasing