Project Plan: Preparation of Benchmark SAS Data Set using a Round Robin Approach to Developing a Consensus Standard Set
Aim:
Generate a set of SAS data sets that can be used to benchmark different approaches to predicting SAS profiles from atomic coordinates.
[Download: Project Plan Documentation]
[Download : Letter sent to wwPDB leadership initiating this project, 11June2019]
Specific Objectives:
• Measure up to 5 proteins with known structures at different SAS beam lines using a common batch for each protein and appropriate standard buffer(s).
• Compare data sets for consistency.
• Agree a set of data to be made available to the research community to benchmark methods for predicting scattering profiles, along with the measurement protocol and sources of material via a publicly accessible Website(s).
• Published a consensus white paper on the results of the exercise.
Analysis and Publication:
• Project coordinator Jill Trewhella will receive, initially in confidence, individual data sets as I(q) vs q with I(q) on an absolute scale (cm-1) and associated errors for [Sample+Solvent], [Solvent], and [Sample+Solvent] - [Solvent] and perform an initial comparison.
• This initial comparison would include direct comparison of scaled I(q) vs q, Guinier Rg, P(r) profiles with Rg, Porod volume and relative I(0) compared to expected based on known molecular weight within each set from a given instrument.
• Any outliers identified in the above comparison will be discussed in confidence with the contributor to provide the opportunity to address any issues that might be revealed.
• With the agreement of each contributor, their data will be part of a set that will be made available to all project participants to develop a set of consensus findings.
• Individual participants will decide if they want to contribute their data to the benchmarking set or subset; the aim is to include data over the widest q-range possible with accurate error propagation, hence minimal data manipulation, on all four proteins.
• Data in the benchmarking set or subset will be deposited in a public archive with complete information on their source and measurement protocol and may include some SAXS-WAXS profiles developed by combining different measurements. In this latter case, the contributing measurements to generate the SAXS-WAXS profile will also be deposited.
• The consensus findings of the exercise will be published as white paper, all data contributing will be fully documented per the 2017 publication guidelines http://scripts.iucr.org/cgi-bin/paper?S2059798317011597.
Full Details about the selected proteins, material supply, measurements to be taken, and data to be supplied can be found in the following document: [Project PDF]
