2WI8 | pdb_00002wi8

Crystal structure of the triscatecholate siderophore binding protein FeuA from Bacillus subtilis


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18PROTEIN WAS CRYSTALLIZED FROM 30% (V/V) JEFFAMINE ED-2001 PH 7.0, 100 MM HEPES, PH 8.0; THEN SOAKED IN MOTHER LIQUOR CONTAINING 30% (V/V) GLYCEROL FOR CRYOPROTECTION
Crystal Properties
Matthews coefficientSolvent content
1.9235.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.71α = 90
b = 54.71β = 90
c = 177.66γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2008-02-16MSINGLE 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
11.5519.2698.10.0617.54.739175-316.698
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)
11.551.6495.90.374.84.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2PHZ1.5519.233817599997.580.182670.181780.180.215440.22RANDOM20.372
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]
-0.25-0.250.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.511
r_dihedral_angle_3_deg12.687
r_dihedral_angle_4_deg11.566
r_dihedral_angle_1_deg5.221
r_scangle_it3.973
r_scbond_it2.425
r_mcangle_it1.393
r_angle_refined_deg1.349
r_mcbond_it0.855
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.511
r_dihedral_angle_3_deg12.687
r_dihedral_angle_4_deg11.566
r_dihedral_angle_1_deg5.221
r_scangle_it3.973
r_scbond_it2.425
r_mcangle_it1.393
r_angle_refined_deg1.349
r_mcbond_it0.855
r_nbtor_refined0.312
r_symmetry_hbond_refined0.216
r_nbd_refined0.202
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.117
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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 Atoms2198
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing