Dataset DOI: 10.5061/dryad.6m905qgbn

Description of the data and file structure

Here, we present mass photometer data from the main and supplementary figures of the manuscript, “EXO1 promotes the meiotic MLH1-MLH3 endonuclease through conserved interactions with MLH1, MSH4 and DNA”. The files uploaded include all the information needed to plot the panels as indicated in the attached main and supplementary figures and the file names.

Mass photometer data

The dataset comprises:

• Raw mass photometry files (.mp) in the open HDF5 file format.
• Video files (.mp4) showing the real-time movies captured by the mass photometer.

Each .mp file and its corresponding .mp4 file are associated with an individual result shown in the main and supplementary figures of the manuscript, including the specific protein construct(s) indicated in each description. However, these files may be viewed, analyzed, or repurposed independently of the manuscript as well.

File Information

Main Figures

1. Figure 3d top: EXO1 (D173A)-FLAG
   • Main_Fig_3d_top.mp (raw mass photometry data)
   • Main_Fig_3d_top.mp4 (movie)
2. Figure 3d middle: MutSγ (MSH4-Strep-MSH5-His)
   • Main_Fig_3d_middle.mp (raw mass photometry data)
   • Main_Fig_3d_middle.mp4 (movie)
3. Figure 3d bottom: EXO1 (D173A)-FLAG and MutSγ complex
   • Main_Fig_3d_bottom.mp (raw mass photometry data)
   • Main_Fig_3d_bottom.mp4 (movie)

Supplementary Figures

1.      Supplementary Figure 4b left: EXO1-1-390-FLAG

• Sup_Fig_4b_right.mp (raw mass photometry data)
• Sup_Fig_4b_right.mp4 (movie)

2.      Supplementary Figure 4b right: EXO1-1-352-FLAG

• Sup_Fig_4b_right.mp (raw mass photometry data)

• Sup_Fig_4b_right.mp4 (movie)

3.      Supplementary Figure 5f left: EXO1 (W371E Y375E)

• Sup_Fig_5f_left.mp (raw mass photometry data)

• Sup_Fig_5f_left.mp4 (movie)

4.      Supplementary Figure 5f right: EXO1 1-390 (W371E Y375E)

• Sup_Fig_5f_right.mp (raw mass photometry data)

• Sup_Fig_5f_right.mp4 (movie)

5.      Supplementary Figure 6b top left: MSH4 (F288E)-MSH5

• Sup_Fig_6b_top_left.mp (raw mass photometry data)

• Sup_Fig_6b_top_left.mp4 (movie)

6.      Supplementary Figure 6b top right: MSH4 (F225E F288E)-MSH5

• Sup_Fig_6b_top_right.mp (raw mass photometry data)

• Sup_Fig_6b_top_right.mp4 (movie)

7.      Supplementary Figure 6b bottom left: MSH4 (T238E Y244D F288E)-MSH5

• Sup_Fig_6b_bottom_left.mp (raw mass photometry data)

• Sup_Fig_6b_bottom_left.mp4 (movie)

8.      Supplementary Figure 6b bottom right: MSH4 (F225E)-MSH5

• Sup_Fig_6b_bottom_right.mp (raw mass photometry data)

• Sup_Fig_6b_bottom_right.mp4 (movie)

9.      Supplementary Figure 7c left: EXO1-KD-KD-FLAG

• Sup_Fig_7c_left.mp (raw mass photometry data)

• Sup_Fig_7c_left.mp4 (movie)

10.   Supplementary Figure 7c right: EXO1 1-390-KD-KD-FLAG

• Sup_Fig_7c_right.mp (raw mass photometry data)

• Sup_Fig_7c_right.mp4 (movie)

 In total, there are 13 .mp files and 13 .mp4 files.

Opening and Viewing the Data

Raw Mass Photometry Files (.mp)

• The .mp files follow the open HDF5 file format.
• Recommended software:
  • DiscoverMP (Refeyn Ltd) is the proprietary software used to analyze the data and export the videos.
  • Open-source options: Any HDF5-compatible viewer such as HDFView (from the HDF Group)

Using DiscoverMP is recommended for reproducing exact mass assignments and visualization of the molecular count histograms.

Movie Files (.mp4)

• Standard video files that can be opened with most media players (e.g., VLC, QuickTime, Windows Media Player).
• Each .mp4 is a 1-minute video of molecules binding to the coverslip surface as recorded by the mass photometer.

Interpreting the Data

When opened in DiscoverMP or HDF5-compatible software, .mp files contain:

• Reflection-interference contrast measurements for individual molecules over time.
• Mass (kDa): Determined by calibrating the reflection signal with a protein standard (NativeMark™ Unstained Protein Standard, Invitrogen).
• Counts: The number of molecules detected within a specific mass range or throughout the movie.

The typical unit for molecular mass in these files is kilodaltons (kDa). The “counts” are unitless (simply the accumulated counts of detected particles).

Additional Notes

• Data Collection: AcquireMP (Refeyn Ltd, version 2023 Rl.l) was used to collect all raw data.
• Data Analysis: DiscoverMP (Refeyn Ltd, version v2023 Rl.2) was used to analyze the .mp files and to create the histogram plots.
• For reproducibility, open the .mp files in DiscoverMP to obtain molecular mass distributions and corresponding counts.
• The .mp4 videos serve as a visual reference of molecules interacting with the coverslip surface during the 1-minute recording