3DWA

Crystal structure of the B-subunit of the AB5 toxin from E. coli


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.229316%(w/v) PEG 3350, 100mM sodium cacodylate, 200mM ammonium fluoride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2261.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.63α = 90
b = 97.63β = 90
c = 165.36γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-BAPS14-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.08484.2245985
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.084

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 DIFFRACTIONSADTHROUGHOUT2.08448.843610236186.980.191820.18940.23626RANDOM28.1
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]
-0.98-0.49-0.981.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.235
r_dihedral_angle_3_deg16.597
r_dihedral_angle_4_deg15.297
r_dihedral_angle_1_deg8.387
r_scangle_it4.293
r_scbond_it3.011
r_mcangle_it2.045
r_angle_refined_deg1.702
r_mcbond_it1.393
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.235
r_dihedral_angle_3_deg16.597
r_dihedral_angle_4_deg15.297
r_dihedral_angle_1_deg8.387
r_scangle_it4.293
r_scbond_it3.011
r_mcangle_it2.045
r_angle_refined_deg1.702
r_mcbond_it1.393
r_nbtor_refined0.308
r_symmetry_vdw_refined0.273
r_nbd_refined0.216
r_xyhbond_nbd_refined0.167
r_chiral_restr0.128
r_symmetry_hbond_refined0.128
r_bond_refined_d0.019
r_gen_planes_refined0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4546
Nucleic Acid Atoms
Solvent Atoms340
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement