This codebook.txt file was generated on wilsonkm on 2021/05/11 ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Replica-averaged orientational-restrained ensembles of DWORF and P15A-DWORF in lipid bilayers 2. Author Information Associate or Co-investigator Contact Information Name: Venkateswara Reddy Uddigiri Institution: University of Minnesota Twin Cities Associate or Co-investigator Contact Information Name: Daniel K Weber Institution: University of Minnesota Twin Cities Associate or Co-investigator Contact Information Name: Songlin Wang Institution: University of Minnesota Twin Cities Associate or Co-investigator Contact Information Name: Erik K Larsen Institution: University of Minnesota Twin Cities Associate or Co-investigator Contact Information Name: Tata Gopinath Institution: University of Minnesota Twin Cities Associate or Co-investigator Contact Information Name: Alfonso De Simone Institution: Imperial College London & University of Naples “Federico II” Associate or Co-investigator Contact Information Name: Seth Robia Institution: Loyola University Chicago Principal Investigator Contact Information Name: Gianluigi Veglia Institution: University of Minnesota Twin Cities Email: vegli001@umn.edu 3. Date of data collection: 2019-07-01 to 2021-05-03 4. Geographic location of data collection: RAOR-MD data: Imperial College London 5. Information about funding sources that supported the collection of the data: Sponsorship: National Institutes of Health (R01HL143816, R01HL092321); American Heart Association (19POST34420009) -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal 2. Links to publications that cite or use the data: Reddy, U. V., Weber, D. K., Wang, S., Larsen, E. K., Gopinath, T., De Simone, A., Robia, S. & Veglia, G. A Kink in DWORF Helical Structure Controls the Activation of the Sarcoplasmic Reticulum Ca2+-ATPase. 2021. bioRxiv, https://doi.org/10.1101/2021.05.05.442831 3. Links to other publicly accessible locations of the data: GROMACS patch for applying relpica-averaged orientational restraints: https://github.com/maximosanz/modelSSNMR 4. Links/relationships to ancillary data sets: OS-ssNMR Data: Biological Magnetic Resonance Data Bank, Accessions 50778 and 50779 Low energy structures: Protein Data Bank, Accession 7MPA 5. Was data derived from another source? If yes, list source(s): 6. Recommended citation for the data: Uddigiri, V. R., Weber, D., Wang, S., Wang, E. K., Gopinath, T., De Simone, A., Robia, S., & Veglia, G. (2021). Replica-averaged orientational-restrained ensembles of DWORF and P15A-DWORF in lipid bilayers [Data set]. Data Repository for the University of Minnesota (DRUM). https://doi.org/10.13020/2VF6-Y268 --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: DWORF_WT_lipids.gro Short description: GROMACS topology file for ensemble of wild-type DWORF in a DMPC/POPC membrane B. Filename: DWORF_WT_ensemble_lipids.xtc Short description: GROMACS trajectory file for ensemble of wild-type DWORF in a DMPC/POPC membrane C. Filename: DWORF_WT_protein.gro Short description: GROMACS topology file for ensemble of wild-type DWORF in a DMPC/POPC membrane (protein atoms only) D. Filename: DWORF_WT_ensemble_protein.xtc Short description: GROMACS trajectory file for ensemble of wild-type DWORF in a DMPC/POPC membrane (protein atoms only) E. Filename: DWORF_P15A_lipids.gro Short description: GROMACS topology file for ensemble of DWORF-P15A mutant in a DMPC/POPC membrane F. Filename: DWORF_P15A_ensemble_lipids.xtc Short description: GROMACS trajectory file for ensemble of DWORF-P15A mutant in a DMPC/POPC membrane G. Filename: DWORF_P15A_protein.gro Short description: GROMACS topology file for ensemble of DWORF-P15A mutant in a DMPC/POPC membrane (protein atoms only) H. Filename: DWORF_P15A_ensemble_protein.xtc Short description: GROMACS trajectory file for ensemble of DWORF-P15A mutant in a DMPC/POPC membrane (protein atoms only) 2. Relationship between files: DWORF_WT_lipids.gro: Toplogy file to load with DWORF_WT_ensemble_lipids.xtc trajectory file DWORF_WT_protein.gro: Toplogy file to load with DWORF_WT_ensemble_protein.xtc trajectory file DWORF_P15A_lipids.gro: Toplogy file to load with DWORF_P15A_ensemble_lipids.xtc trajectory file DWORF_P15A_protein.gro: Toplogy file to load with DWORF_P15A_ensemble_protein.xtc trajectory file 3. Additional related data collected that was not included in the current data package: None 4. Are there multiple versions of the dataset? No If yes, list versions: Name of file that was updated: i. Why was the file updated? ii. When was the file updated? Name of file that was updated: i. Why was the file updated? ii. When was the file updated? -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Fully detailed in associated citation. 2. Methods for processing the data: Fully detailed in associated citation. 3. Instrument- or software-specific information needed to interpret the data: Fully detailed in associated citation. 4. Standards and calibration information, if appropriate: Fully detailed in associated citation. 5. Environmental/experimental conditions: Fully detailed in associated citation. 6. Describe any quality-assurance procedures performed on the data: Fully detailed in associated citation. 7. People involved with sample collection, processing, analysis and/or submission: Daniel K. Weber: Collection and processing of RAOR-MD data. Analysis of ensembles. Submission of data. Máximo Sanz-Hernández, Alfonso De Simone: RAOR-MD calculation of ensembles and analysis. Gianluigi Veglia: Submission of data. Tata Gopinath, Songlin Wang, Venkateswara Reddy Uddigiri, Erik K. Larsen: Collection and processing of experimental data guiding ROAR-MD calcualtions.