3DWP

Crystal structure of the B-subunit of the AB5 toxin from E. Coli with Neu5Gc


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.229316% PEG 3350, 100mM sodium cacodylate, 200mM ammonium fluoride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.261.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.9α = 90
b = 96.9β = 90
c = 165.622γ = 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
1ROTATING ANODERIGAKU RUH3R

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
12.283.9239693
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.22.32

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 REPLACEMENTTHROUGHOUT2.223.9737666201989.040.190810.188180.23992RANDOM22.463
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]
-0.6-0.3-0.60.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.922
r_dihedral_angle_3_deg16.078
r_dihedral_angle_4_deg14.377
r_dihedral_angle_1_deg7.162
r_scangle_it2.569
r_scbond_it1.629
r_angle_refined_deg1.468
r_mcangle_it1.205
r_mcbond_it0.704
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.922
r_dihedral_angle_3_deg16.078
r_dihedral_angle_4_deg14.377
r_dihedral_angle_1_deg7.162
r_scangle_it2.569
r_scbond_it1.629
r_angle_refined_deg1.468
r_mcangle_it1.205
r_mcbond_it0.704
r_nbtor_refined0.303
r_symmetry_vdw_refined0.204
r_symmetry_hbond_refined0.203
r_nbd_refined0.199
r_xyhbond_nbd_refined0.172
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.005
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 Atoms4532
Nucleic Acid Atoms
Solvent Atoms480
Heterogen Atoms190

Software

Software
Software NamePurpose
REFMACrefinement