Nature - USA (2020-09-24)

2

nature research | reporting summary

October 2018

Field-specific reporting

Please select the one below that is the best fit for your research. If you are not sure, read the appropriate sections before making your selection.

Life sciences Behavioural & social sciences Ecological, evolutionary & environmental sciences

For a reference copy of the document with all sections, see nature.com/documents/nr-reporting-summary-flat.pdf

Life sciences study design

All studies must disclose on these points even when the disclosure is negative.

Sample size For quantitative studies, such as the Zinc Ejection Assay and HPLC Analysis of Model Reactions, a sample size of at least n = 3 was sought for

each data point. Crosslinking experiments were carried out in triplicate and and validated via SDS-PAGE analysis, with representative data

shown. For all other experiments, chemical syntheses and protein modification reactions were carried out as single experiments (n = 1) for

each condition, and reported values (conversions and yields) should be regarded as semi-quantitative; single experiments were deemed

appropriate for these synthetic reactions as they are viewed in the context of many 100s of comparable reactions from which consistent

trends and hence conclusions were drawn.

Data exclusions No data excluded

Replication Crosslinking experiments were carried out in triplicate and and validated via SDS-PAGE analysis, with representative data shown. For all other

experiments, chemical syntheses and protein modification reactions were carried out as single experiments (n = 1) for each condition, and

reported values (conversions and yields) should be regarded as semi-quantitative; single experiments were deemed appropriate for these

synthetic reactions as they are viewed in the context of many 100s of comparable reactions from which consistent trends and hence

conclusions were drawn. Independent replicates were consistent and reliably afforded the same conclusions.

Randomization Not applicable - no experimental groups were involved.

Blinding Not applicable - no group allocation was involved.

Reporting for specific materials, systems and methods

We require information from authors about some types of materials, experimental systems and methods used in many studies. Here, indicate whether each material,

system or method listed is relevant to your study. If you are not sure if a list item applies to your research, read the appropriate section before selecting a response.

Materials & experimental systems

n/a Involved in the study

Antibodies

Eukaryotic cell lines

Palaeontology

Animals and other organisms

Human research participants

Clinical data

Methods

n/a Involved in the study

ChIP-seq

Flow cytometry

MRI-based neuroimaging

Antibodies

Antibodies used DYKDDDDK (FLAG) Tag Monoclonal Antibody (eBioscience, catalogue number 14-6681-82, clone FG4R, lot number 1981531),

Monoclonal Anti-polyHistidine-Alkaline Phosphatase (Sigma-Aldrich, catalogue number A5588, clone HIS-1, lot number

085M4836V), Histone H3 Antibody (Cell Signaling Technology, catalogue number 3638S, clone 96C10, lot number 10), Goat Anti-

Mouse IgG H&L Alkaline Phosphatase (Sigma-Aldrich, catalog number A3562, polyclonal, lot number SLCB8722), Anti-Mouse IgG

(H+L) HRP Conjugate (Promega, catalogue number W4021, polyclonal, lot number 0000306114). cAbLys3 was not used as a

reagent but as a substrate for reaction.

Antibody dilutions: FLAG antibody (1:1000), poly-His (1:2000), Histone H3 (1:1000), Goat Anti-Mouse IgG Alkaline Phosphatase

(1:10,000), Anti-Mouse IgG HRP Conjugate (1:2,500).

Validation Antibody Validation Details:

DYKDDDDK (FLAG) Tag Monoclonal Antibody: Source and Use: eBioscience, catalogue number 14-6681-82, clone FG4R, lot

number 1981531, dilution 1:1,000. [ Supplier link: https://www.thermofisher.com/antibody/product/DYKDDDDK-Tag-Antibody-

clone-FG4R-Monoclonal/14-6681-82. ] Supplier verification: Antibody tested by western blot, no other validation given. Note: A

separate supplier (Invitrogen, catalog # MA1-91878-1MG) of the same antibody clone (FG4R) verified the antibody by cell

treatment to ensure that the antibody binds to the antigen stated. [ Link: https://www.thermofisher.com/antibody/product/

MA1-91878-1MG.html?CID=AFLCA-MA1-91878-1MG ]. Supplier suggested applications: Immunoprecipitation (IP), Western Blot