5AD1 | pdb_00005ad1

A complex of the synthetic siderophore analogue Fe(III)-8-LICAM with the CeuE periplasmic protein from Campylobacter jejuni


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A5VPDB ENTRY 5A5V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.2M SODIUM FORMATE, 0.1M BTP BUFFER, PH 8.5, 20% PEG 3350.
Crystal Properties
Matthews coefficientSolvent content
2.6353.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.98α = 90
b = 55.98β = 90
c = 140.08γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.3255.9896.60.08115.9777611.5
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)
11.321.35760.851.33.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 5A5V1.3255.9873860381596.640.141950.140010.150.180560.19RANDOM13.926
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]
-0.270.3-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.308
r_sphericity_free23.585
r_dihedral_angle_3_deg11.812
r_dihedral_angle_4_deg10.188
r_sphericity_bonded9.78
r_dihedral_angle_1_deg5.845
r_rigid_bond_restr4.772
r_scbond_it3.36
r_angle_refined_deg1.96
r_mcangle_it1.867
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.308
r_sphericity_free23.585
r_dihedral_angle_3_deg11.812
r_dihedral_angle_4_deg10.188
r_sphericity_bonded9.78
r_dihedral_angle_1_deg5.845
r_rigid_bond_restr4.772
r_scbond_it3.36
r_angle_refined_deg1.96
r_mcangle_it1.867
r_mcbond_it1.584
r_mcbond_other1.584
r_angle_other_deg0.988
r_chiral_restr0.133
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2239
Nucleic Acid Atoms
Solvent Atoms397
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
PHASERphasing