2WHY

Crystal structure of the triscatecholate siderophore binding protein FeuA from Bacillus subtilis complexed with Ferri-Bacillibactin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PHZPDB ENTRY 2PHZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.2PROTEIN WAS CRYSTALLIZED FROM 30% (V/V) PEG 600, 100 MM PHOSPHATE-CITRATE, PH 5.2; THEN SOAKED IN MOTHER LIQUOR CONTAINING 30% (V/V) GLYCEROL FOR CRYO PROTECTION.
Crystal Properties
Matthews coefficientSolvent content
1.8633.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.53α = 90
b = 63.14β = 110.44
c = 55.53γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2008-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.719.7699.20.0420.13.728022-324.416
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)
11.71.7999.50.523.43.7

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 2PHZ1.719.5125537247299.210.160420.157490.1912RANDOM23.303
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]
0.14-0.57-1.080.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.67
r_dihedral_angle_3_deg13.482
r_dihedral_angle_4_deg9.408
r_dihedral_angle_1_deg5.096
r_scangle_it2.275
r_scbond_it1.45
r_angle_refined_deg1.159
r_angle_other_deg0.864
r_mcangle_it0.85
r_mcbond_it0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.67
r_dihedral_angle_3_deg13.482
r_dihedral_angle_4_deg9.408
r_dihedral_angle_1_deg5.096
r_scangle_it2.275
r_scbond_it1.45
r_angle_refined_deg1.159
r_angle_other_deg0.864
r_mcangle_it0.85
r_mcbond_it0.55
r_symmetry_vdw_other0.228
r_nbd_refined0.21
r_nbd_other0.186
r_nbtor_refined0.176
r_symmetry_hbond_refined0.161
r_nbtor_other0.157
r_symmetry_vdw_refined0.141
r_mcbond_other0.136
r_xyhbond_nbd_refined0.121
r_chiral_restr0.064
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2199
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing