8BXY

FimH in complex with alpha1,6 core-fucosylated oligomannose-3, crystallized in the trigonal space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VCO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92911.1 M Lithium sulphate; 0.1 M Tris-HCl pH 9.0; 10 mM nickel chloride
Crystal Properties
Matthews coefficientSolvent content
2.6553.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.056α = 90
b = 91.056β = 90
c = 79.578γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.987SOLEILPROXIMA 2

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
11.4556.07695.160.0750.0770.0170.999619.32520.115619924.99
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)
11.451.55621.91.8371.9490.6390.6151.616.95

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.4556.07656198148182.8670.1550.15320.205432.691
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]
0.6030.3010.603-1.955
RMS Deviations
KeyRefinement Restraint Deviation
r_rigid_bond_restr23.863
r_dihedral_angle_6_deg17.432
r_scbond_it16.344
r_scangle_it13.632
r_dihedral_angle_3_deg11.962
r_lrange_it10.166
r_dihedral_angle_1_deg8.084
r_dihedral_angle_2_deg5.984
r_mcangle_it5.584
r_mcbond_it5.091
RMS Deviations
KeyRefinement Restraint Deviation
r_rigid_bond_restr23.863
r_dihedral_angle_6_deg17.432
r_scbond_it16.344
r_scangle_it13.632
r_dihedral_angle_3_deg11.962
r_lrange_it10.166
r_dihedral_angle_1_deg8.084
r_dihedral_angle_2_deg5.984
r_mcangle_it5.584
r_mcbond_it5.091
r_angle_refined_deg1.809
r_chiral_restr0.437
r_nbtor_refined0.315
r_symmetry_nbd_refined0.217
r_xyhbond_nbd_refined0.214
r_nbd_refined0.196
r_symmetry_xyhbond_nbd_refined0.159
r_ncsr_local_group_10.113
r_metal_ion_refined0.035
r_bond_refined_d0.016
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2392
Nucleic Acid Atoms
Solvent Atoms345
Heterogen Atoms151

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
PHENIXmodel building
autoPROCdata processing
XDSdata reduction
XSCALEdata scaling
PHASERphasing