Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Escherichia coli) | BL21-RIL | N/A | ||
| Recombinant DNA reagent | SIRT6 (plasmid) | AddGene | #28271 | SIRT6 (PDB: 3PKJ) in pET28a-LIC |
| Recombinant DNA reagent | Mutant SIRT6 (DNA fragment) | SynBio | K170A, R172A, R175A, R178A, R220A, R231A and R248A | |
| Recombinant DNA reagent | Widom601 DNA (plasmid) | Dyer et al., 2004 | Gift from Dr. K. Mohideen-Abdul. | |
| Recombinant DNA reagent | X. laevis H2A, H2B, H3, H4 histones (plasmids) | Luger et al., 1999; Dyer et al., 2004 | Gift from Dr. K. Mohideen-Abdul. | |
| Recombinant DNA reagent | Human H2A.Z.1 (plasmid) | AddGene | #42629 | H2A.Z.1 in pET28a |
| Antibody | H3K27ac (rabbit monoclonal) |
CellSignaling | #8173 S | Diluted: 1:1000 |
| Antibody | H3K9ac (rabbit polyclonal) |
Abcam | Ab4441 | Diluted: 1:2500 |
| Antibody | H3 (mouse monoclonal) |
CellSignaling | #14269 S | Diluted: 1:1000 |
| Software, algorithm | SerialEM | v4.1 | Automated data collection | |
| Software, algorithm | EPU | Thermo Fisher | v3.4 | Automated data collection |
| Software, algorithm | Warp | Warp | v1.0.9 | Micrograph preprocessing |
| Software, algorithm | cryoSPARC | cryoSPARC | v4 | Image analysis |
| Software, algorithm | RELION | RELION | v3.1 | Image analysis |
| Software, algorithm | crYOLO | crYOLO | v1.9.6 | Particle picking |
| Software, algorithm | cryoDRGN | cryoDRGN | v1.1 | Image analysis – structural flexibility analysis |
| Software, algorithm | DeepEMhancer | DeepEMhancer | v0.8 | Map sharpening |
| Software, algorithm | UCSF Chimera/ChimeraX | UCSF ChimeraX | v1.16/1.6 | Rigid body fitting, visualisation and figures |
| Software, algorithm | Isolde | Isolde | v1.6 | Flexible fitting, model refinement |
| Software, algorithm | PHENIX | PHENIX | v1.21 | Model refinement |
| Software, algorithm | AMBER20 suit | AMBER20 | MD simulations |