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X-ray structure of the complex between staphylococcal enterotoxin B, T cell receptor and major histocompatibility complex class II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGA PDB ENTRIES 1OGA CHAINS D AND E, 2IAL CHAIN A, 1SEB CHAINS A, B AND C experimental model PDB 2IAL PDB ENTRIES 1OGA CHAINS D AND E, 2IAL CHAIN A, 1SEB CHAINS A, B AND C experimental model PDB 1SEB PDB ENTRIES 1OGA CHAINS D AND E, 2IAL CHAIN A, 1SEB CHAINS A, B AND C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 8% PEG 20000, 0.1 M SODIUM CITRATE PH 5.5, 0.09 M MAGNESIUM CHLORIDE
Crystal Properties Matthews coefficient Solvent content 2.9 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.35 α = 90 b = 217.65 β = 99.82 c = 101.41 γ = 90
Symmetry Space Group P 1 21 1
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 315r 2011-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.9 48.7 99 0.08 13.1 3.2 61924 2 82.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 99.9 0.58 2.3 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1OGA CHAINS D AND E, 2IAL CHAIN A, 1SEB CHAINS A, B AND C 2.9 29.23 61848 3134 98.98 0.2338 0.2329 0.2454 0.2511 0.2641 RANDOM 65.03
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] -4.7586 -11.4009 5.0533 -0.2947
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.84 t_omega_torsion 1.47 t_angle_deg 0.87 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.84 t_omega_torsion 1.47 t_angle_deg 0.87 t_bond_d 0.007 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16279 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 6
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PHASER phasing