Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2

  1. Qi Peng
  2. Ruchao Peng
  3. Bin Yuan
  4. Jingru Zhao
  5. Min Wang
  6. Xixi Wang
  7. Qian Wang
  8. Yan Sun
  9. Zheng Fan
  10. Jianxun Qi
  11. George F. Gao
  12. Yi Shi

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    SciScore for 10.1101/2020.04.23.057265: (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

    Software and Algorithms
    SentencesResources
    The data was automatically collected using SerialEM software (http://bio3d.colorado.edu/SerialEM/).
    SerialEM
    suggested: (SerialEM, RRID:SCR_017293)
    Image processing: The image drift and anisotropic magnification was corrected using MotionCor2 (Zheng et al., 2017).
    MotionCor2
    suggested: (MotionCor2, RRID:SCR_016499)
    The model was manually corrected for local fit in COOT (Emsley et al., 2010) and the sequence register was corrected based on alignment.
    COOT
    suggested: (Coot, RRID:SCR_014222)
    The initial model was refined in real space using PHENIX (Adams et al., 2010) with the secondary structural restraints and Ramachandran restrains applied.
    PHENIX
    suggested: (Phenix, RRID:SCR_014224)
    The model was further adjusted and refined iteratively for several rounds aided by the stereochemical quality assessment using MolProbity (Chen et al., 2010).
    MolProbity
    suggested: (MolProbity, RRID:SCR_014226)
    Structural figures were rendered by either CHIMERA (Pettersen et al., 2004) or PyMOL (https://pymol.org/).
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)
    Images were taken using a Vilber Fusion system and analyzed with the Image J software.
    Image J
    suggested: (ImageJ, RRID:SCR_003070)

    Results from OddPub: Thank you for sharing your data.

    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: Please consider improving the rainbow (“jet”) colormap(s) used on page 30. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

    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.

  2. Version published to 10.1016/j.celrep.2020.107774
  3. Version published to 10.1101/2020.04.23.057265v1 on bioRxiv