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SEC-SAXS Mail-in Instructions the basics

Introduction    Registration    Samples    Spreadsheet    Shipping    Data    Resources    Citing   

Introduction mail-in HT-SAXS at SIBYLS

SEC-SAXS workflow

Below is a schematic diagram of the SEC-SAXS workflow that you may take advantage of at the SIBYLS beamline 12.3.1 at the Advanced Light Source in Berkeley:


Secsaxsintro

Coupling SEC with SAXS

Separation of analytes is typically accomplished by size-exclusion chromatography (SEC) using an Agilent 1260 series HPLC with a Shodex analytical column at a flow rate of 0.5 ml/min using a your favorite buffer with the maximum of pH 7.5. Eluent is split 2 to 1 between X-ray synchrotron radiation and a series of four inline analytical instruments:


  1. Aglient 1260 series multiple wavelength detector (MWD)
  2. Wyatt Dawn Helos multi-angle light scattering (MALS) detector
  3. Wyatt DyanPro Titan quasi-elastic light scattering (QELS) detector
  4. Wyatt Optilab rEX refractometer, see the diagram below:

Wyatt_optilab_rex_refractometer


Samples are then examined using small-angle X-ray scattering (SAXS) as they come off of the column with λ=1.03 Å incident light at a sample to detector distances of 1.5 m. This results in scattering vectors, q, ranging from 0.013 Å -1 to 0.5 Å-1, where the scattering vector is defined as q = 4πsinθ/λ and 2θ is the measured scattering angle.

3 s exposures are collected for each frame over the course of 40 min. SEC-SAXS chromatographs are generated and initial SAXS curves are analyzed using ScÅtter.

Additionally, UV, MALS, QELS, and differential refractive index data is collected and analyzed using Wyatt Astra 6 software.


Registration request beamtime in 4 easy steps

1. Request mail-in account

All SIBYLS mail-in SAXS users must first register for a mail-in account:

This action is performed on this website. If you have never registered or are not logged in there will be a request link in the upper right hand corner of the page. You may also click the button below to get started.

Request Mail-in Account

2. Register with ALS

All users must also register with the ALS User Office:

You will not have access to your data until you are registered.

Register with ALS

3. Submit RAPIDD Proposal

Users must also submit one ALS RAPIDD proposal for every three mail-in uses:

Make sure you submit a "RAPIDD" proposal and not a "General User" proposal. RAPPID proposals are for record keeping only and will not affect your chances of using our service. So far, the high-throughput capabilities of our endstation have allowed us to accept every user that has requested mail-in SAXS time.

RAPIDD Proposals

4. Book mail-in slot

After requesting a mail-in account, registering with the ALS User Office and submitting a RAPIDD proposal, you may book a mail-in slot for beamtime:

If you are logged in to this site there will be a link to book mail-in time in the upper right hand corner.

In addition, the button below will lead you to the login or the mail-in booking page depending on your login status.

Login

Samples information on sample, column and buffer requirements

Prepare sample

Each shift is limited to 7 samples using 1 column and 1 buffer.

Each column run has the following sample and buffer requirements:

  1. A sample with a minimum volume of 60 µl
  2. 50 ml of 10x SEC buffer

The sample concentration should be from 3-10 mg/ml with smaller molecules requiring higher concentrations. Ideally, the sample should be prepared in a buffer that is identical or very similar to the SEC buffer.

For SEC buffers, the salt concentration must not exceed 500 mM and the pH of the buffer must be less than 7.5 to be accepted. If glycerol is desired, the concentration should not exceed 2%.

Please use small concentrations of other stabilizers such as glucose, ATP, etc. to minimize scattering background and to avoid high column-pressures.

Size-exclusion columns

A list of available columns with a summary of their properties are shown in the Table below. Please specify the columns to use in your experiments.

Available Size-exclusion Columns

Product Name Exclusion Limit (Protein kDa) Particle Size (μm) Maximum Pore Size (Å) Column Size (mm) ID x L
PROTEIN KW-802.5 150 5 400 8 x 300
PROTEIN KW-803 700 5 400 8 x 300
PROTEIN KW-804 1000 7 1500 8 x 300

Spreadsheet sample entry and template

Upload sample information

    The following information in a spreadsheet is required:
  1. sample name
  2. sample volume
  3. sample concentration
  4. the expected molecular weight of each constituent
  5. the estimated morphology (globular, rod, flexible, monomer, dimer, trimer)
  6. the SEC-buffer
  7. a brief description of any sample preparation, desired alterations to the aforementioned experimental parameters or other comments in the comments column

  8. Download Example

    Download Template

Example spreadsheet

Sample Name Sample Volume (μl) Sample Concentration (mg/ml) Expected Molecular Weight (kDa) Estimated Morphology Comments
hammel_prot1 60 5 Subunit A: 150, B: 90 Globular Heterodimer X-ray Sensitive
hammel_dna1 60 2 18 Rod dsDNA w/ Thymine glycol
hammel_protdna1 60 7 258 Dimer:dsDNA Complex DNA Binds Weakly
SEC Buffer 20 mM Tris-Cl, 150 mM NaCl, 2% glycerol, pH 7.0
Column Shodex 803

Please send this information as an excel file with

filename: shiftdate_SEC-SAXS_username.xlsx

by email to mhammel@lbl.gov and DJR@lbl.gov with

subject line: "SEC-SAXS SPREADSHEET shiftdate username"

Use 'MMDDYY' format for the shiftdate.


Shipping how to package and ship your samples and buffers

Ship sample overnight

We recommended that samples are shipped in standard Eppendorf PCR tubes together with 10x buffer using 4 °C cold packs (NOT frozen) in a styrofoam shipping container. Tightly pack the styrofoam box by surrounding assembly with more cold packs. While in some cases it is ok if the packs are frozen, do not allow the tubes to touch them. 

DO NOT ship wet ice.

Clearly label the outside of your shipping box with the temperature of your samples. This is extremely important if a shipping delay occurs.

Lastly, please provide us with a shipping tracking number.

Shipping address

Ship samples overnight to arrive at SIBYLS on the first day of your shift:

    SHIPPING ADDRESS:

  • Lawrence Berkeley Lab
  • 
ATTN: Daniel Rosenberg / SIBYLS 12.3.1
  • 1 Cyclotron Road 
MS 6R2136
  • Berkeley, CA 94720
  • Phone: (510) 495-3116

Data what happens after your sample arrives

Results and Analysis

We will provide a merged SAXS curve for each sample together with short report including SAXS parameters and P(r) function to assess the quality of data. We will also provide a SEC-MALS report for further quality control.

After the data has been successfully collected, users have a choice as to the amount of SIBYLS staff involvement in processing and analyzing the results. Our team uses a variety of programs and decades of combined experience to assist you in your analysis. If you desire to process your results directly from un-subtracted SAXS profiles, you are welcome to transfer raw un-subtracted SAXS curve files as follows:

local> ssh username@kona.als.lbl.gov
[username@kona ~]$ cp -R /data/secsaxs/Results/shiftdate_SEC-SAXS_username .

where the shiftdate is in format "MMDDYY"

Your data will then be copied to your home directory on our kona server. To transfer files to your local computer, you may go into your local target directory and either remote sync rsync or secure copy scp the files from kona:

local>cd path/your_data_directory
local>scp -rp username@kona.als.lbl.gov:/data/secsaxs/Results/shiftdate_SEC-SAXS_username .

Or you may use sftp or other tools to transfer data to your local computer.

This is helpful in particular if you want to reprocess unsubtracted data in ScÅtter. The ScÅtter tutorial will help you navigate data processing.

Feedback

We are continuing to improve our systems with the aim of making data of higher quality. Please provide us with constructive feedback. For additional information please feel free to contact:

  • Daniel Rosenberg
  • Research Associate
  • DJR@lbl.gov
  • Michal Hammel, Ph.D
  • SAXS Scientist
  • Mhammel@lbl.gov

Online Webinars

We regularly present online webinars to highlight new SAXS features, and how to address and solve specific problems that occur during SAXS data collection and processing:


Citing the key to keep SIBYLS running to serve you

Cite SIBYLS in published papers

Please cite all relevant SIBYLS beamline papers below in the 'References' section of your journal article or book chapter

  • Dyer KN, Hammel M, Rambo RP, Tsutakawa SE, Rodic I, Classen S, Tainer JA, Hura GL (2014) “High-Throughput SAXS for the Characterization of Biomolecules in Solution: A Practical Approach” Methods Mol. Biol. 1091, 245-58. (Specific Methods paper for HT-SAXS at SIBYLS)
  • Classen S, et al. (2013) “Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source” J. Appl. Crystallogr. 46(Pt 1), 1-13. (SIBYLS Beamline hardware)
  • Hura GL, et al. (2009) "Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)" Nature Methods 6, 606–612. (General High Throughput SAXS)
  • Putnam CD1, Hammel M, Hura GL, Tainer JA (2007) "Solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution” Q. Rev. Biophys. 40, 191-285. (General SAXS)

Acknowledge SIBYLS

Please include the following in the 'Acknowledgements' section of your journal article or book chapter when using data generated at SIBYLS:

"This work was conducted at the Advanced Light Source (ALS), a national user facility operated by Lawrence Berkeley National Laboratory on behalf of the Department of Energy, Office of Basic Energy Sciences, through the Integrated Diffraction Analysis Technologies (IDAT) program, supported by DOE Office of Biological and Environmental Research. Additional support comes from the National Institute of Health project ALS-ENABLE (P30 GM124169) and a High-End Instrumentation Grant S10OD018483."

These citations and acknowledgments are absolutely essential in keeping the mail-in SAXS program funded and the beamline continually repaired and upgraded, as well as to provide access to experienced staff and the development of new technologies, such as SEC-SAXS.