4RGO

Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 14G8


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529880 mM sodium cacodylate, pH 6.5, 16% w/v PEG8000, 160 mM magnesium acetate, 20% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7254.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.576α = 90
b = 85.292β = 90
c = 115.017γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2012-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.979NSLSX4C

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
11.810099.30.08238.512.47767777133-3
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)
11.81.8389.90.5611.84.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 1SE4, 3FFD, AND 3D9A1.842.657764776413383098.410.144330.141950.18903RANDOM23.132
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]
0.311.6-1.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.2
r_dihedral_angle_4_deg18.85
r_dihedral_angle_3_deg12.245
r_dihedral_angle_1_deg6.2
r_scangle_it4.055
r_scbond_it2.746
r_mcangle_it1.619
r_angle_refined_deg1.403
r_rigid_bond_restr1.127
r_mcbond_it0.974
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.2
r_dihedral_angle_4_deg18.85
r_dihedral_angle_3_deg12.245
r_dihedral_angle_1_deg6.2
r_scangle_it4.055
r_scbond_it2.746
r_mcangle_it1.619
r_angle_refined_deg1.403
r_rigid_bond_restr1.127
r_mcbond_it0.974
r_angle_other_deg0.835
r_mcbond_other0.297
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5140
Nucleic Acid Atoms
Solvent Atoms908
Heterogen Atoms4

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling