2G9H

Crystal Structure of Staphylococcal Enterotoxin I (SEI) in Complex with a Human MHC class II Molecule


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SXT1SXT and 1DHL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529810% dioxane, 1.2 mM (NH4)2SO4 and 100 mM Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.9368.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.395α = 90
b = 99.933β = 92
c = 72.917γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATERIGAKU RAXIS IVOsmic mirrors2005-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12404.0572140
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)
122.070.3783.937089

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1SXT and 1DHL229.796919029491000.214880.214880.213270.2524RANDOM34.003
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]
-1.17-0.062.3-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.95
r_dihedral_angle_4_deg20.833
r_dihedral_angle_3_deg17.013
r_dihedral_angle_1_deg6.628
r_scangle_it2.716
r_scbond_it1.727
r_angle_refined_deg1.451
r_mcangle_it1.113
r_mcbond_it0.638
r_symmetry_vdw_refined0.361
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.95
r_dihedral_angle_4_deg20.833
r_dihedral_angle_3_deg17.013
r_dihedral_angle_1_deg6.628
r_scangle_it2.716
r_scbond_it1.727
r_angle_refined_deg1.451
r_mcangle_it1.113
r_mcbond_it0.638
r_symmetry_vdw_refined0.361
r_nbtor_refined0.312
r_symmetry_hbond_refined0.253
r_nbd_refined0.206
r_xyhbond_nbd_refined0.19
r_metal_ion_refined0.162
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4856
Nucleic Acid Atoms
Solvent Atoms460
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata scaling
PHASERphasing