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Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SEB PDB ENTRIES 3SEB AND 2ICW experimental model PDB 2ICW PDB ENTRIES 3SEB AND 2ICW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.43 49.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.954 α = 90 b = 160.37 β = 90 c = 186.265 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 TOROIDAL FOCUSING MIRROR 2010-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.95 121.531 94.7 0.199 16.75 13.9 69820 66122 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.06 99 0.793 4.5 13.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 3SEB AND 2ICW 2.95 46.57 66380 61375 3244 92.46 0.24705 0.24705 0.24607 0.242 0.26547 0.2605 RANDOM 37.936
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] -1.56 0.93 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.167 r_dihedral_angle_4_deg 22.196 r_dihedral_angle_3_deg 16.7 r_dihedral_angle_1_deg 6.41 r_scangle_it 2.119 r_angle_refined_deg 1.259 r_scbond_it 1.222 r_mcangle_it 1.009 r_angle_other_deg 0.852 r_mcbond_it 0.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.167 r_dihedral_angle_4_deg 22.196 r_dihedral_angle_3_deg 16.7 r_dihedral_angle_1_deg 6.41 r_scangle_it 2.119 r_angle_refined_deg 1.259 r_scbond_it 1.222 r_mcangle_it 1.009 r_angle_other_deg 0.852 r_mcbond_it 0.518 r_mcbond_other 0.08 r_chiral_restr 0.07 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21868 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 43
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling