Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Escherichia coli) | dnaX | doi: 10.1093/nar/14.20.8091 |
Uniprot ID: P06710 | |
| Gene (Human Immunodeficiency Virus Type 1) | gag-pol | doi: 10.1089/aid.1987.3.57 |
Uniprot ID: P04585 | |
| Strain, strain background (Escherichia coli) | MRE600 | ATCC | ATCC #29417, (NCTC #8164, NCIB #10115) | E. coli strain K-12 that lacks the RNase I activity |
| Strain, strain background (Escherichia coli) | DH5α competent cell | Thermo Fisher Scientific | Catalog #: 18265017 | |
| Genetic reagent (Escherichia coli) | tRNA | Chemical Block | tRNAPhe tRNATyrtRNAfMet tRNAMettRNAGlu tRNAValtRNALys tRNAArg | |
| Genetic reagent (Escherichia coli) | Total tRNA from E. coli MRE600 | Sigma-Aldrich | Catalog #: 10109541001 | |
| Transfected construct (Escherichia coli) | pSP64 poly (A) | Promega | Catalog #: P1241 | |
| Biological sample (Escherichia coli) | ribosome (30S, 50S and 70S) | doi: 10.1016/j.jmb.2007.04.042 doi: 10.1073/pnas.1520337112 |
||
| Recombinant DNA reagent | SacI-HF | New England Biolabs | Catalog #: R3156 | |
| Recombinant DNA reagent | BglII | New England Biolabs | Catalog #: R0144 | |
| Recombinant DNA reagent | HindIII-HF | New England Biolabs | Catalog #: R3104 | |
| Recombinant DNA reagent | T4 DNA ligase | New England Biolabs | Catalog #: M0202 | |
| Peptide, recombinant protein | elongation factor Tu (EF-Tu) | doi: 10.1016/j.jmb.2007.04.042 |
||
| Peptide, recombinant protein | elongation factor G (EF-G) | doi: 10.1016/j.jmb.2007.04.042 |
||
| Peptide, recombinant protein | T7 polymerase | doi: 10.1073/pnas.95.2.515 |
||
| Commercial assay or kit | Plasmid Miniprep System | Promega | Catalog #: A1223 | |
| Commercial assay or kit | Gel and PCR Clean-Up System | Promega | Catalog #: A9281 | |
| Commercial assay or kit | DNA oligo synthesis | INTEGRATED DNA TECHNOLOGIES (IDT) | ||
| Commercial assay or kit | DNA sequencing | ACGT, INC | ||
| Chemical compound, drug | puromycin | Sigma-Aldrich | Catalog #: P8833 | |
| Chemical compound, drug | cy3 maleimide | Click Chemistry Tools | Catalog #: 1009 | |
| Chemical compound, drug | cy5 maleimide | Click Chemistry Tools | Catalog #: 1004 | |
| Chemical compound, drug | Phenylalanine, L -[2,3,4,5,6-3H]- | PerkinElmer | Catalog #: NET112201MC | |
| Chemical compound, drug | Valine, L-[U-14C]- | PerkinElmer | Catalog #: NEC291EU050UC | |
| Chemical compound, drug | Methionine, L-[35S]- | PerkinElmer | Catalog #: NEG009T001MC | |
| Chemical compound, drug | Glutamic Acid, L-[3,4–3H]- | PerkinElmer | Catalog #: NET490001MC | |
| Chemical compound, drug | Tyrosine, L -[ring-3,5 |
PerkinElmer | Catalog #: NET127001MC | |
| Software, algorithm | smFRET data acquisition and analysis package | Taekjip Ha’s laboratory website at Johns Hopkins University (http://ha.med.jhmi.edu/resources/) | ||
| Software, algorithm | IDL | ITT, INC. (https://www.harrisgeospatial.com/Software-Technology/IDL) |
||
| Software, algorithm | HaMMy | Taekjip Ha’s laboratory website at Johns Hopkins University (http://ha.med.jhmi.edu/resources/) doi: 10.1529/biophysj.106.082487 |
||
| Software, algorithm | SerialEM | (https://bio3d.colorado.edu/SerialEM/) doi: 10.1016/j.jsb.2005.07.007 |
||
| Software, algorithm | cisTEM | (https://cistem.org/) doi: 10.7554/eLife.35383 | ||
| Software, algorithm | Phenix-1.17.1–3660 | (https://www.phenix-online.org/) doi:10.1107/S2059798319011471 | ||
| Software, algorithm | Coot v0.9 pre-EL | Part of CCPEM 1.3.0 suite (https://www.ccpem.ac.uk/index.php) doi:10.1107/S2059798317007859 |
||
| Software, algorithm | PyMol 2.3.2 | Schrödinger, LLC (https://pymol.org) |