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Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 14G8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SE4 PDB ENTRIES 1SE4, 3FFD, AND 3D9A experimental model PDB 3FFD PDB ENTRIES 1SE4, 3FFD, AND 3D9A experimental model PDB 3D9A PDB ENTRIES 1SE4, 3FFD, AND 3D9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 80 mM sodium cacodylate, pH 6.5, 16% w/v PEG8000, 160 mM magnesium acetate, 20% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.576 α = 90 b = 85.292 β = 90 c = 115.017 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 MAR CCD 165 mm 2012-02-14 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 1.8 100 99.3 0.082 38.5 12.4 77677 77133 -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 1.8 1.83 89.9 0.561 1.8 4.6
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, 3FFD, AND 3D9A 1.8 42.65 77647 76413 3830 98.41 0.14433 0.14195 0.1517 0.18903 0.1971 RANDOM 23.132
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] 0.31 1.6 -1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.2 r_dihedral_angle_4_deg 18.85 r_dihedral_angle_3_deg 12.245 r_dihedral_angle_1_deg 6.2 r_scangle_it 4.055 r_scbond_it 2.746 r_mcangle_it 1.619 r_angle_refined_deg 1.403 r_rigid_bond_restr 1.127 r_mcbond_it 0.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.2 r_dihedral_angle_4_deg 18.85 r_dihedral_angle_3_deg 12.245 r_dihedral_angle_1_deg 6.2 r_scangle_it 4.055 r_scbond_it 2.746 r_mcangle_it 1.619 r_angle_refined_deg 1.403 r_rigid_bond_restr 1.127 r_mcbond_it 0.974 r_angle_other_deg 0.835 r_mcbond_other 0.297 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5140 Nucleic Acid Atoms Solvent Atoms 908 Heterogen Atoms 4
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling