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A complex of the synthetic siderophore analogue Fe(III)-5-LICAM with CeuE (H227L variant), a periplasmic protein from Campylobacter jejuni.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.1M PCB buffer, pH 8, 25% PEG 1500 +cryo 33% PEG 1500 in well solution
Crystal Properties Matthews coefficient Solvent content 2.53 51.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.696 α = 82.09 b = 62.881 β = 74.67 c = 69.867 γ = 77.6
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 PSI PILATUS 6M 2016-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
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 1.9 67.13 95.9 0.102 0.991 6.2 3.4 70811
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 1.9 1.94 96 0.956 0.418 1.3 3.5
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 3ZKW 1.9 67.13 67360 3451 95.85 0.17355 0.17143 0.1808 0.21499 0.2231 RANDOM 34.815
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] 0.76 -0.79 0.14 -0.75 1.23 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.078 r_dihedral_angle_3_deg 15.013 r_dihedral_angle_4_deg 11.591 r_long_range_B_other 7.33 r_long_range_B_refined 7.326 r_dihedral_angle_1_deg 6.319 r_scangle_other 6.277 r_scbond_it 4.149 r_scbond_other 4.148 r_mcangle_it 3.798
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.078 r_dihedral_angle_3_deg 15.013 r_dihedral_angle_4_deg 11.591 r_long_range_B_other 7.33 r_long_range_B_refined 7.326 r_dihedral_angle_1_deg 6.319 r_scangle_other 6.277 r_scbond_it 4.149 r_scbond_other 4.148 r_mcangle_it 3.798 r_mcangle_other 3.798 r_mcbond_it 2.858 r_mcbond_other 2.858 r_angle_refined_deg 1.85 r_angle_other_deg 1.041 r_chiral_restr 0.114 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 6586 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing