8RMI

Crystal structure of ferrioxamine transporter FoxA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6I96 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2932.1 M Ammonium Sulphate 0.1 M HEPES pH 7.5 0.7% n-octyl-beta-d-glucoside
Crystal Properties
Matthews coefficientSolvent content
2.4950.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.515α = 90
b = 93.515β = 90
c = 177.817γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-08-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.9763PETRA III, EMBL c/o DESYP14 (MX2)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.4880.9993.60.1480.1530.040.99913.114.916422
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.482.851.5461.5980.3990.851

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.4880.991557684550.420.221190.21870.26818RANDOM88.379
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]
0.720.360.72-2.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.076
r_long_range_B_other13.741
r_long_range_B_refined13.74
r_dihedral_angle_2_deg10.02
r_dihedral_angle_1_deg9.233
r_scangle_other8.032
r_mcangle_it6.314
r_mcangle_other6.313
r_scbond_it5.34
r_scbond_other5.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.076
r_long_range_B_other13.741
r_long_range_B_refined13.74
r_dihedral_angle_2_deg10.02
r_dihedral_angle_1_deg9.233
r_scangle_other8.032
r_mcangle_it6.314
r_mcangle_other6.313
r_scbond_it5.34
r_scbond_other5.14
r_mcbond_it4.017
r_mcbond_other4.017
r_angle_refined_deg1.985
r_angle_other_deg0.936
r_chiral_restr0.086
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.005
r_gen_planes_other0.004
r_dihedral_angle_4_deg
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 Atoms5325
Nucleic Acid Atoms
Solvent Atoms39
Heterogen Atoms155

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing