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Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 20B1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SE4 PDB ENTRIES 1SE4 AND 1JHK experimental model PDB 1JHK PDB ENTRIES 1SE4 AND 1JHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.1 M HEPES sodium, pH 7.5, 20% w/v PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.69 54.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.467 α = 90 b = 83.669 β = 91.4 c = 174.731 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 MAR CCD 165 mm 2011-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.979 NSLS X4C
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 2.689 174.679 99.7 0.158 16.1 7.2 44051 43919 -3
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 2.689 2.75 95.8 0.503 2.5 4.9
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 (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 1SE4 AND 1JHK 2.689 174.679 45493 43728 2194 96.12 0.22777 0.22514 0.2228 0.27656 0.2693 RANDOM 34.005
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] -1.01 -0.11 1.06 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.197 r_dihedral_angle_4_deg 17.279 r_dihedral_angle_3_deg 15.266 r_dihedral_angle_1_deg 5.995 r_scangle_it 1.166 r_angle_refined_deg 1.054 r_angle_other_deg 0.765 r_scbond_it 0.703 r_mcangle_it 0.469 r_mcbond_it 0.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.197 r_dihedral_angle_4_deg 17.279 r_dihedral_angle_3_deg 15.266 r_dihedral_angle_1_deg 5.995 r_scangle_it 1.166 r_angle_refined_deg 1.054 r_angle_other_deg 0.765 r_scbond_it 0.703 r_mcangle_it 0.469 r_mcbond_it 0.239 r_chiral_restr 0.064 r_mcbond_other 0.043 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10380 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling