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Structure of Staphylococcal Enterotoxin B bound to two neutralizing antibodies, 14G8 and 6D3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RGO PDB ENTRIES 4RGO AND 3GI8 experimental model PDB 3GI8 PDB ENTRIES 4RGO AND 3GI8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 298 0.1 M phosphate/citrate, pH 4.2, 6.7% w/v PEG3000, 0.5 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.75 55.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 301.331 α = 90 b = 109.818 β = 94.53 c = 82.782 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 100 CCD ADSC QUANTUM 315r 2012-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 2.698 100 98.9 0.094 19.9 4.3 74028 73214 -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 2.698 2.75 98.2 0.741 1.8 3.8
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 (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 4RGO AND 3GI8 2.698 45.71 74137 72447 3611 97.72 0.24195 0.24005 0.2356 0.27756 0.2691 RANDOM 52.094
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 0.32 2.39 -2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.088 r_dihedral_angle_3_deg 17.246 r_dihedral_angle_4_deg 16.276 r_dihedral_angle_1_deg 7.134 r_angle_refined_deg 1.447 r_angle_other_deg 0.999 r_scangle_it 0.712 r_scbond_it 0.558 r_mcangle_it 0.347 r_mcbond_it 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.088 r_dihedral_angle_3_deg 17.246 r_dihedral_angle_4_deg 16.276 r_dihedral_angle_1_deg 7.134 r_angle_refined_deg 1.447 r_angle_other_deg 0.999 r_scangle_it 0.712 r_scbond_it 0.558 r_mcangle_it 0.347 r_mcbond_it 0.21 r_mcbond_other 0.105 r_chiral_restr 0.081 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 16749 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling