1. SciScore for 10.1101/2020.06.17.156554: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Experimental Models: Cell Lines
    Cloning and protein expression: The coding sequence for the 3a protein from SARS-Cov-2 was codon optimized for Spodoptera frugiperda (Sf9 cells) and synthesized (IDT, Newark, NJ).
    suggested: CLS Cat# 604328/p700_Sf9, RRID:CVCL_0549)
    Constructs (2 μg) were transfected into HEK293 cells on glass coverslips using Fugene HD (Promega, Madison, WI) per manufacturer’s instructions.
    suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)
    Software and Algorithms
    To calculate the total number of liposomes, we quantified the total number of liposomes using auto segmentation on MetaXpress 6 from brightfield images.
    suggested: (MetaXpress, RRID:SCR_016654)
    All statistical tests were performed using Prism (GraphPad).
    suggested: (PRISM, RRID:SCR_005375)
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Cryo-EM data processing: For the apo 3a dimer, motion-correction and dose-weighting were performed on all 6,309 movies using RELION 3.1’s implementation of MotionCor2, and 2x “binned” to 1.137 Å per pixel49–51.
    suggested: (RELION, RRID:SCR_016274)
    suggested: (MotionCor2, RRID:SCR_016499)
    A set of 86,479 particles were identified, polished in RELION3.1 and refined in cryoSPARC v2 with subsequent homogeneous and non-uniform refinement54 jobs (maps were low-pass filtered to an initial resolution where TM density was still visible (6-9 Å), and the dynamic mask was tightened with the near (2-5 Å) and far (3-9 Å) parameters), yielding a map with overall resolution of 3.6 Å.
    suggested: (cryoSPARC, RRID:SCR_016501)
    Molprobity61 was used to evaluate the stereochemistry and geometry of the structure for subsequent rounds of manual adjustment in Coot and refinement in Phenix.
    suggested: (Phenix, RRID:SCR_014224)
    Cavity measurements were made with HOLE64 implemented in Coot.
    suggested: (Coot, RRID:SCR_014222)
    Figures were prepared using PyMOL, Chimera, ChimeraX66, Fiji, Prism, GNU Image Manipulation Program, and Adobe Photoshop and Illustrator software.
    suggested: (PyMOL, RRID:SCR_000305)
    suggested: (Fiji, RRID:SCR_002285)
    Image Manipulation Program
    suggested: (GNU Image Manipulation Program, RRID:SCR_003182)
    Adobe Photoshop
    suggested: (Adobe Photoshop, RRID:SCR_014199)
    suggested: (Adobe Illustrator, RRID:SCR_010279)
    The samples were excited with 488nm argon laser and image analysis was performed using ImageJ.
    suggested: (ImageJ, RRID:SCR_003070)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

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