Supporting_Information.zip

<br>Supporting Information Summary for:<br>Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells<br>Arnab Sengupta, Greggory M. Rice, and Kevin M. WeeksDepartment of ChemistryUniversity of North Carolina<br><br>This supporting information contains data and analysis files used in the 16S ribosome RING-MaP paper.<br><br>The [S1_File] archive contains the following:<br>-- [Analysis_pipeline]: Software programs used to calculate per-nucleotide reactivity rates, and correlation analysis. Files ending in .py can be executed in Python. This folder also contains a README.txt file containing specific details on using the software. Additional .txt files contain example data that can be used to test the programs. The folder named excluded nucleotides contains an indexed list of nucleotides excluded from analysis due to high background mutation. Most of these high background nucleotides are from SNPs in the multiple copies of the ribosomal gene present in E. coli.<br>-- [ArcPlot_CorrelationData_FS2]: RING correlation data and arc-plot diagrams for all treatment conditions and replicates. Treatment conditions are indicated by labels ex (extracted), IC (in-cell), Rif (rifampicin), Spc (spectinomycin), RifSpc (rifampicin and spectinomycin). Replicate information is indicated by numbers 1 and 2. Merged and average replicate data are also included as .txt and .pdf files. ArcPlot diagrams used in Fig. S2 were prepared using these data.<br>-- [Gephi_Data_F2BC_FS3]: Contains network analysis input files. Gephi output files use RING correlation data for network visualization. Files ending in .gephi can be opened in the Gephi software to visualize network diagrams. IC analysis files have information degree analysis and modularity class information under the different treatment conditions. The .svg files contains plots of correlation data superimposed on 16S RNA secondary structure maps. Files with the label "r" contain data for rifampicin treatment, "rs" contain data for rifampicin and spectinomycin treatment. Numerical labels (1-9) represent modularity class. Additional files contain information of nucleotide coloring by network community on the 16S secondary structure. <br>-- [PyMol_Sessions]: Pymol sessions files (.pse) used to prepare Figs. 2C, 3D, 3E, 4A, 4B, 4C, 4D, and 5. Sessions contain defined objects for distinct states and features. Scripts used to create pymol sessions, starting from the pdb file, are also included.<br><br>The file [S1_Data] contains per-nucleotide DMS reactivity data for conditions including extracted, in-cell, +Rif, and +RifSpc treatment.<br><br>The file [S2_Data] contains the underlying data used to prepare figures 2A, 3, S2, and S3.<br>