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Staphylococcus aureus exfoliative toxin D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q8GAX8-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 ammonium sulfate, sodium acetate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.597 α = 90 b = 122.597 β = 90 c = 60.514 γ = 120
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 PILATUS 6M 2022-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.75 43.06 99.8 0.043 0.014 35.6 10.2 52340
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 0.782 0.253 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 AF-Q8GAX8-F1 1.75 43.06 49640 2684 99.83 0.16241 0.1615 0.1756 0.17962 0.1908 RANDOM 32.164
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.064 r_dihedral_angle_1_deg 6.917 r_long_range_B_refined 6.284 r_long_range_B_other 6.234 r_scangle_other 4.68 r_dihedral_angle_2_deg 4.203 r_mcangle_it 3.268 r_mcangle_other 3.267 r_scbond_it 2.848 r_scbond_other 2.846
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.064 r_dihedral_angle_1_deg 6.917 r_long_range_B_refined 6.284 r_long_range_B_other 6.234 r_scangle_other 4.68 r_dihedral_angle_2_deg 4.203 r_mcangle_it 3.268 r_mcangle_other 3.267 r_scbond_it 2.848 r_scbond_other 2.846 r_mcbond_it 2.054 r_mcbond_other 2.05 r_angle_refined_deg 1.139 r_angle_other_deg 0.643 r_chiral_restr 0.057 r_gen_planes_other 0.007 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1910 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing