Structure of replicating SARS-CoV-2 polymerase

  1. Hauke S. Hillen
  2. Goran Kokic
  3. Lucas Farnung
  4. Christian Dienemann
  5. Dimitry Tegunov
  6. Patrick Cramer

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  1. ScreenIT

    SciScore for 10.1101/2020.04.27.063180: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    RandomizationThe experiments were not randomized, and the investigators were not blinded to allocation during experiments and outcome assessment.
    BlindingThe experiments were not randomized, and the investigators were not blinded to allocation during experiments and outcome assessment.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The PCR product containing codon optimized nsp12 was cloned into the modified pFastBac vector 438-C (a gift from S. Gradia, UC Berkeley, Addgene: 55220
    Addgene
    suggested: (Addgene, RRID:SCR_002037)
    418k particles (82%) from the class representing the complex were exported from cryoSPARC to RELION 3.030.
    RELION
    suggested: (RELION, RRID:SCR_016274)
    There, all particles were refined in 3D against the reconstruction previously obtained in cryoSPARC, using a mask including only the core part of the polymerase and a short segment of upstream RNA to obtain a 3.1 Å reconstruction.
    cryoSPARC
    suggested: (cryoSPARC, RRID:SCR_016501)
    Particles were re-extracted at 1.3 Å/ px in a bigger box in Warp to accommodate distant parts of the RNA.
    Warp
    suggested: (Warp, RRID:SCR_018071)
    Figures were prepared with PyMol and Chimera33.
    PyMol
    suggested: (PyMOL, RRID:SCR_000305)

    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.

  2. Version published to 10.1038/s41586-020-2368-8
  3. ScreenIT

    SciScore for 10.1101/2020.04.27.063180: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.RandomizationThe experiments were not randomized, and the investigators were not blinded to allocation during experiments and outcome assessment.BlindingThe experiments were not randomized, and the investigators were not blinded to allocation during experiments and outcome assessment.Power Analysisnot detected.Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The PCR product containing codon optimized nsp12 was cloned into the modified pFastBac vector 438-C ( a gift from S. Gradia , UC Berkeley , Addgene: 55220
    Addgene
    suggested: (Addgene, SCR_002037)
    418k particles (82%) from the class representing the complex were exported from cryoSPARC to RELION 3.030.
    RELION
    suggested: (RELION, SCR_016274)
    There, all particles were refined in 3D against the reconstruction previously obtained in cryoSPARC, using a mask including only the core part of the polymerase and a short segment of upstream RNA to obtain a 3.1 Å reconstruction.
    cryoSPARC
    suggested: (cryoSPARC, SCR_016501)
    Particles were re-extracted at 1.3 Å/ px in a bigger box in Warp to accommodate distant parts of the RNA.
    Warp
    suggested: (Warp, SCR_018071)
    Figures were prepared with PyMol and Chimera33.
    PyMol
    suggested: (PyMOL, SCR_000305)

    Results from OddPub: Thank you for sharing your data.

    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 is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, please follow this link.

  4. Version published to 10.1101/2020.04.27.063180v1 on bioRxiv