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Crystal Structure of Staphylococcal Enterotoxin I (SEI) in Complex with a Human MHC class II Molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SXT 1SXT and 1DHL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 10% dioxane, 1.2 mM (NH4)2SO4 and 100 mM Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.93 68.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.395 α = 90 b = 99.933 β = 92 c = 72.917 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE RIGAKU RAXIS IV Osmic mirrors 2005-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 40 4.05 72140
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 2.07 0.378 3.93 7089
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 (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 1SXT and 1DHL 2 29.79 69190 2949 100 0.21488 0.21488 0.21327 0.2141 0.2524 0.2499 RANDOM 34.003
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 -0.06 2.3 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.95 r_dihedral_angle_4_deg 20.833 r_dihedral_angle_3_deg 17.013 r_dihedral_angle_1_deg 6.628 r_scangle_it 2.716 r_scbond_it 1.727 r_angle_refined_deg 1.451 r_mcangle_it 1.113 r_mcbond_it 0.638 r_symmetry_vdw_refined 0.361
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.95 r_dihedral_angle_4_deg 20.833 r_dihedral_angle_3_deg 17.013 r_dihedral_angle_1_deg 6.628 r_scangle_it 2.716 r_scbond_it 1.727 r_angle_refined_deg 1.451 r_mcangle_it 1.113 r_mcbond_it 0.638 r_symmetry_vdw_refined 0.361 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.253 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.19 r_metal_ion_refined 0.162 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4856 Nucleic Acid Atoms Solvent Atoms 460 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement CrystalClear data scaling PHASER phasing