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The crystal structure of DfoC, the desferrioxamine biosynthetic pathway acetyltransferase/Non-Ribosomal Peptide Synthetase (NRPS)-Independent Siderophore (NIS) from the fire blight disease pathogen Erwinia amylovora
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X0O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 0.1 M TRIS-HCl, 0.2 M MgCl2, 0.06 M Ammonium citrate, 10% PEG 8K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.17 α = 90 b = 156.35 β = 95.57 c = 93.81 γ = 90
Symmetry Space Group P 1 21 1
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 2015-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97625 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.11 78.18 99.79 0.04 12 3.4 123387
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.165
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 2x0o 2.11 78.18 117229 6119 99.79 0.2227 0.22055 0.2348 0.264 0.2731 RANDOM 50.695
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] -0.19 -4.14 -3.38 4.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.286 r_dihedral_angle_4_deg 17.873 r_dihedral_angle_3_deg 14.775 r_dihedral_angle_1_deg 6.853 r_long_range_B_refined 6.659 r_long_range_B_other 6.643 r_scangle_other 4.898 r_mcangle_it 4.433 r_mcangle_other 4.432 r_scbond_it 3.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.286 r_dihedral_angle_4_deg 17.873 r_dihedral_angle_3_deg 14.775 r_dihedral_angle_1_deg 6.853 r_long_range_B_refined 6.659 r_long_range_B_other 6.643 r_scangle_other 4.898 r_mcangle_it 4.433 r_mcangle_other 4.432 r_scbond_it 3.431 r_scbond_other 3.431 r_mcbond_it 3.189 r_mcbond_other 3.189 r_angle_refined_deg 1.679 r_angle_other_deg 1.04 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 11584 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing