5O7O

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X0O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72930.1 M TRIS-HCl, 0.2 M MgCl2, 0.06 M Ammonium citrate, 10% PEG 8K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.17α = 90
b = 156.35β = 95.57
c = 93.81γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97625DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.1178.1899.790.04123.4123387
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.112.165

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2x0o2.1178.18117229611999.790.22270.220550.264RANDOM50.695
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]
-0.19-4.14-3.384.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.286
r_dihedral_angle_4_deg17.873
r_dihedral_angle_3_deg14.775
r_dihedral_angle_1_deg6.853
r_long_range_B_refined6.659
r_long_range_B_other6.643
r_scangle_other4.898
r_mcangle_it4.433
r_mcangle_other4.432
r_scbond_it3.431
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.286
r_dihedral_angle_4_deg17.873
r_dihedral_angle_3_deg14.775
r_dihedral_angle_1_deg6.853
r_long_range_B_refined6.659
r_long_range_B_other6.643
r_scangle_other4.898
r_mcangle_it4.433
r_mcangle_other4.432
r_scbond_it3.431
r_scbond_other3.431
r_mcbond_it3.189
r_mcbond_other3.189
r_angle_refined_deg1.679
r_angle_other_deg1.04
r_chiral_restr0.098
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms11584
Nucleic Acid Atoms
Solvent Atoms425
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing