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New insights into the P186 flip and oligomeric state of Staphylococcus aureus exfoliative toxin E: implications for the exfoliative mechanism
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5C2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 4 M Sodium Formate
Crystal Properties Matthews coefficient Solvent content 2.45 49.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.744 α = 90 b = 97.744 β = 90 c = 116.657 γ = 90
Symmetry Space Group P 43 21 2
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 2M 2019-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.45870 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.61 48.92 100 0.075 0.078 1 17.85 13.314 138763 36.271
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.61 1.71 99.9 2.322 2.419 0.455 0.95 12.74
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 5C2Z 1.61 48.92 69347 3650 99.93 0.2158 0.2142 0.2236 0.2479 0.2547 RANDOM 33.64
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_2_deg 35.098 r_dihedral_angle_4_deg 23.272 r_dihedral_angle_3_deg 15.361 r_dihedral_angle_1_deg 7.844 r_angle_refined_deg 1.776 r_angle_other_deg 1.418 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.098 r_dihedral_angle_4_deg 23.272 r_dihedral_angle_3_deg 15.361 r_dihedral_angle_1_deg 7.844 r_angle_refined_deg 1.776 r_angle_other_deg 1.418 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3838 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XDS data scaling PHASER phasing PDB_EXTRACT data extraction