5ADV

The Periplasmic Binding Protein CeuE of Campylobacter jejuni preferentially binds the iron(III) complex of the Linear Dimer Component of Enterobactin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZKWPDB ENTRY 3ZKW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
190.1 M PCB (SODIUM PROPIONATE, SODIUM CACODYLATE, BIS-TRIS PROPANE, 2:1:2) BUFFER PH 9.0 25% (W/V) PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.250.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.07α = 83.09
b = 63.09β = 76.9
c = 67.16γ = 79.21
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.147.5996.30.097.72.1510942
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1695.40.811.72.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3ZKW2.165.1948582251096.250.220390.218310.26021RANDOM31.158
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]
-1.45-1.330.8-0.281.821.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.738
r_dihedral_angle_3_deg16.758
r_dihedral_angle_4_deg13.184
r_long_range_B_refined6.19
r_long_range_B_other6.19
r_dihedral_angle_1_deg6.034
r_scangle_other4.457
r_mcangle_it3.596
r_mcangle_other3.596
r_scbond_it2.872
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.738
r_dihedral_angle_3_deg16.758
r_dihedral_angle_4_deg13.184
r_long_range_B_refined6.19
r_long_range_B_other6.19
r_dihedral_angle_1_deg6.034
r_scangle_other4.457
r_mcangle_it3.596
r_mcangle_other3.596
r_scbond_it2.872
r_scbond_other2.872
r_mcbond_it2.406
r_mcbond_other2.405
r_angle_refined_deg1.656
r_angle_other_deg1.298
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.007
r_gen_planes_other0.006
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 AtomsNumber
Protein Atoms6598
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction