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Crystal structure of Staphylococcal Superantigen-Like protein 11 in complex with FB127
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RDG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 50 mM Tris-HCl pH 8.5, 50 mM lithium sulphate, 50 mM sodium sulphate, 30% PEG 400
Crystal Properties Matthews coefficient Solvent content 4.26 71.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.37 α = 90 b = 101.37 β = 90 c = 65.23 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS EIGER2 XE 9M 2020-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.979 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.137 36.4 99.83 0.1858 0.993 9.44 9.8 21715
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.193 99.75 0.926
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.137 52.413 21715 1023 99.825 0.203 0.2011 0.2054 0.2363 0.2395 49.034
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] 2.458 1.229 2.458 -7.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.94 r_dihedral_angle_6_deg 13.566 r_lrange_other 9.181 r_lrange_it 9.17 r_dihedral_angle_1_deg 7.246 r_scangle_it 7.06 r_scangle_other 7.054 r_dihedral_angle_2_deg 5.245 r_scbond_it 4.699 r_scbond_other 4.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.94 r_dihedral_angle_6_deg 13.566 r_lrange_other 9.181 r_lrange_it 9.17 r_dihedral_angle_1_deg 7.246 r_scangle_it 7.06 r_scangle_other 7.054 r_dihedral_angle_2_deg 5.245 r_scbond_it 4.699 r_scbond_other 4.644 r_mcangle_it 4.406 r_mcangle_other 4.405 r_mcbond_it 3.068 r_mcbond_other 3.061 r_angle_refined_deg 1.831 r_angle_other_deg 1.305 r_chiral_restr_other 0.375 r_symmetry_xyhbond_nbd_refined 0.243 r_nbd_refined 0.224 r_nbd_other 0.2 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.173 r_symmetry_nbd_refined 0.147 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.084 r_symmetry_xyhbond_nbd_other 0.028 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1539 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building