5A5V | pdb_00005a5v

A complex of the synthetic siderophore analogue Fe(III)-6-LICAM with the CeuE periplasmic protein from Campylobacter jejuni


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A1JPDB ENTRY 5A1J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
160.1 M PCB BUFFER, PH 7, 25% PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.1943.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.37α = 90
b = 66.08β = 90
c = 68.96γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-02-14MSINGLE 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
12.0444.961000.269.67.9184671.5
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)
12.042.091001.241.78.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 5A1J2.0444.971743798899.930.216180.213460.220.265280.27RANDOM23.378
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]
0.03-0.050.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.345
r_dihedral_angle_3_deg16.285
r_dihedral_angle_4_deg15.938
r_dihedral_angle_1_deg6.33
r_long_range_B_refined4.166
r_long_range_B_other4.123
r_scangle_other3.058
r_mcangle_other2.39
r_mcangle_it2.388
r_scbond_it1.959
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.345
r_dihedral_angle_3_deg16.285
r_dihedral_angle_4_deg15.938
r_dihedral_angle_1_deg6.33
r_long_range_B_refined4.166
r_long_range_B_other4.123
r_scangle_other3.058
r_mcangle_other2.39
r_mcangle_it2.388
r_scbond_it1.959
r_scbond_other1.958
r_angle_refined_deg1.635
r_mcbond_it1.594
r_mcbond_other1.585
r_angle_other_deg0.836
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2214
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
PHASERphasing