5ADW

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
180.1 M MMT (DL-MALIC ACID, MES, TRIS, 1:2:2) BUFFER, PH 8.0, 25% (W/V) PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.4850.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.461α = 83.36
b = 63.021β = 76.57
c = 67.011γ = 78.24
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2014-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
11.945.7698.10.117.54.4702792
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)
11.91.9496.10.92.24.2

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 3ZKW1.965.0166562349597.780.226760.22480.26407RANDOM42.232
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]
-1.58-1.620.39-1.110.992.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.449
r_dihedral_angle_4_deg18.855
r_dihedral_angle_3_deg16.108
r_long_range_B_refined8.083
r_long_range_B_other8.082
r_dihedral_angle_1_deg6.583
r_scangle_other6.304
r_mcangle_it5.315
r_mcangle_other5.314
r_scbond_it4.415
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.449
r_dihedral_angle_4_deg18.855
r_dihedral_angle_3_deg16.108
r_long_range_B_refined8.083
r_long_range_B_other8.082
r_dihedral_angle_1_deg6.583
r_scangle_other6.304
r_mcangle_it5.315
r_mcangle_other5.314
r_scbond_it4.415
r_scbond_other4.414
r_mcbond_it3.954
r_mcbond_other3.954
r_angle_refined_deg1.775
r_angle_other_deg1.39
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.008
r_gen_planes_other0.007
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 Atoms6581
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction