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1.93 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus in Complex with Sialyl-Lewis X.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V05
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 Protein: 7.4mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: PEGsII (F12), 0.8M Lithium chloride, 0.1M Tris (pH 8.5), 32% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.88 34.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.64 α = 90 b = 108.199 β = 90 c = 167.655 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 MARMOSAIC 300 mm CCD Mirrors 2014-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97875 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.93 30 99.7 0.074 0.074 19.3 4.9 61498 61498 -3 26.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.96 100 0.552 0.552 3 4.9 3076
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 (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 3V05 1.93 28.83 56257 56257 2997 99.68 0.17106 0.17106 0.16855 0.1758 0.21829 0.2218 RANDOM 34.297
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] -1.26 0.26 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.512 r_dihedral_angle_4_deg 12.867 r_dihedral_angle_3_deg 10.993 r_long_range_B_refined 6.855 r_long_range_B_other 6.79 r_scangle_other 4.541 r_dihedral_angle_1_deg 3.714 r_scbond_it 2.895 r_scbond_other 2.895 r_mcangle_it 2.697
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.512 r_dihedral_angle_4_deg 12.867 r_dihedral_angle_3_deg 10.993 r_long_range_B_refined 6.855 r_long_range_B_other 6.79 r_scangle_other 4.541 r_dihedral_angle_1_deg 3.714 r_scbond_it 2.895 r_scbond_other 2.895 r_mcangle_it 2.697 r_mcangle_other 2.697 r_mcbond_it 1.849 r_mcbond_other 1.849 r_angle_refined_deg 1.637 r_angle_other_deg 0.722 r_chiral_restr 0.099 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6405 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 265
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling