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Crystal structure of Staphylococcal Superantigen-Like protein 11 in complex with SB618
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 291 100 mM HEPES/NaOH pH 7.0, 55% MPD
Crystal Properties Matthews coefficient Solvent content 4.31 71.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.464 α = 90 b = 104.464 β = 90 c = 62.136 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 CCD RIGAKU SATURN 944 Rigaku 2023-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.458 13.813 97.89 0.2502 0.06434 0.996 12.51 9.9 14193 44.13
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 2.458 2.52 92.21 0.507 1.6
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 2.458 13.813 14193 658 97.613 0.175 0.1738 0.1819 0.2077 0.2073 53.223
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] -0.332 -0.166 -0.332 1.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.974 r_dihedral_angle_6_deg 14.771 r_lrange_it 14.371 r_lrange_other 14.371 r_scangle_it 10.214 r_scangle_other 10.212 r_dihedral_angle_2_deg 10.148 r_mcangle_other 8.127 r_mcangle_it 8.126 r_dihedral_angle_1_deg 8.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.974 r_dihedral_angle_6_deg 14.771 r_lrange_it 14.371 r_lrange_other 14.371 r_scangle_it 10.214 r_scangle_other 10.212 r_dihedral_angle_2_deg 10.148 r_mcangle_other 8.127 r_mcangle_it 8.126 r_dihedral_angle_1_deg 8.019 r_scbond_it 6.941 r_scbond_other 6.937 r_mcbond_it 5.43 r_mcbond_other 5.425 r_angle_refined_deg 2.672 r_angle_other_deg 0.926 r_nbd_refined 0.269 r_nbd_other 0.25 r_symmetry_nbd_refined 0.248 r_symmetry_xyhbond_nbd_refined 0.244 r_symmetry_nbd_other 0.215 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.134 r_symmetry_nbtor_other 0.102 r_chiral_restr_other 0.044 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1490 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Coot model building PHASER phasing