Education

X-ray free electron lasers (XFELs) present unique capabilities to revolutionize structural biology and its ability to probe the biological world. As the NASA Apollo era captured a generation's interest in outer space, these unique capabilities have the potential to capture the imagination of students, teachers, and potential scientists interested in inner space; we will foster this effect through our education and diversity programs. The BioXFEL Center is committed to building a culturally and academically diverse, inclusive community of scholars. We aim to make STEM studies exciting and accessible for all students, postdoctoral fellows, faculty and staff.

COVID19 Pandemic Response Initiatives

At the request of the National Science Foundation, BioXFEL will be collecting information on the impact of the current pandemic on our graduate students and postdocs. The Center will be requesting information on the impact on career progression, ability to conduct research, and professional development. Using this information we will make suggestions to NSF Leadership on best practices to remedy the situation by creating new initiatives.

Please fill in the survey below. If you have any additional information to provide that is not requested in the survey, please contact Bill Bauer.

Sample Preparation Guidelines

Important Information for the Participants of the Structural Biology with X-rays Workshop

 

BioSAXS Practical Sessions Information

General Information:

This BioSAXS part of the workshop will be focusing on the introduction to solution X-ray scattering as a method to answer questions in current structural biology research. In addition to the introductory lecture where you will learn the basics of the techniques as well as some of the analysis methods, we will also offer a remote data collection session for SAXS, during which you can measure your own sample (that you must have sent before to SSRL).  On the second day we will also offer a data analysis tutorial, where you can work on your own data (if you have sent samples or some standard protein data we will take during the data collection session)

Here is some information and guidelines we’d like you to follow if you are interested in the SAXS part in order to get you prepared and make these sessions during the workshop run more smoothly.

Laptop computers:

It is highly recommended that students bring their own laptop computer for the remote data collection and data analysis tutorial. Please also make sure that you have the appropriate rights on your machine that you can install software on it. Install the ATSAS suite (http://www.embl-hamburg.de/biosaxs/download.html) from the EMBL group in Hamburg onto your computer (it comes in a windows, mac and linux flavors). Try to see if you can run it (e.g. open primusqt, which is one of the programs in the suite), there won’t be enough time during the workshop to troubleshoot the installation.

For the remote access data collection we use the NX client (https://www.nomachine.com/), which is the same as the one you will use for the crystallography remote access. Please follow their guidelines for the installation and testing.

Also recommended is a program such as PyMol or UCSF Chimera to visualize structural models.

 

Measuring your own SAXS sample:

For those of you who intend to send a sample to SSRL to be measured during the remote session of the workshop please contact Thomas Weiss ( This email address is being protected from spambots. You need JavaScript enabled to view it. ) in order to coordinate the shipment. The samples should be at SSRL no later than Thu. Jan 23, 2020

  • let us know details about the size and composition of your sample (we will need that to reasonably group your measurements together) as well as a short text on the scientific merit and background.
  • please limit your number of samples to be less than four (not counting the dilutions); we cannot guarantee to be able to run more than that per participant during the workshop
  • if you need SEC-SAXS please specify clearly and let us know why you think you need that; for SEC-SAXS we can at most run 2 samples;If you prepare your own sample please follow the sample preparation and shipment guidelines below

Sample Shipment:

  • Unless your protein absolutely doesn’t like to be frozen, send your samples on dry ice. Alternatively you can send your samples also on wet ice using ice packs (but make sure that you mark the storage temperature clearly on the outside of the box, see also below).

    Address the package to:

     your name

    BL4-2, UPR Workshop

    c/o Dr. Thomas Weiss

    SSRL/SLAC Bldg 120

    2575 Sand Hill Rd.

    Menlo Park, CA 94025

    USA

    Again, please clearly mark on the outside of the box whether the samples need to be kept at -80C or at 4C after arrival at SSRL.

    Sample preparation guideline for solution x-ray scattering studies:

    Buffer solution: In solution scattering experiments, the signal arises from the electron density difference (contrast) between solute and solvent solution. One thus must perform successive measurements of the buffer solution alone (buffer) and the protein in the same buffer solution (sample). It is crucial to match the composition of the buffer to that of the sample within a small fraction of 1mM for each chemical component. The use of dialysis outer solution as the buffer solution is ideal, but not required as long as component concentrations can be matched. Alternatively, you can use the run-off buffer from the final size exclusion chromatography step.

    Buffer composition: most buffer solutions (pH 4-10) with or without salt at typical physiological concentrations should be adequate. If you have the choice between high salt and low salt buffer use the one with lower salt concentration, unless your protein is better soluble at the higher salt concentration. Using glycerol up to 5% is OK, but make sure you have the exact matching buffer for the background subtraction. Avoid detergents! Please bring at least several ml of buffer solution.

    Sample concentration: A series of concentrations typically between 0.5mg/mL and 10mg/ml (for instance 1-2-4-8 mg/mL), should be measured to evaluate inter-particle interaction behaviors. A rule of thumb for the high concentration is:

    mol.weight   x  max. concentration ≈100

    However if you sample aggregates before that send your protein in the highest concentration possible without forming detectable aggregates. Determine the concentration of your stock protein solution in advance for concentration scaling during data processing.

    Sample volume: Single set of measurements requires 30μl of a sample aliquot per dilution and takes approximately 3 minutes. A minimum of 3 dilutions per sample should be measured. We will spin down your sample before pipetting the dilution series (unless you tell us explicitly not to) and will pipette off the top so it would be good to have a bit of excess sample if possible.

    Buffer solution: In solution scattering experiments, the signal arises from the electron density difference (contrast) between solute and solvent solution. One thus must perform successive measurements of the buffer solution alone (buffer) and the protein in the same buffer solution (sample). It is crucial to match the composition of the buffer to that of the sample within a small fraction of 1mM for each chemical component. The use of dialysis outer solution as the buffer solution is ideal, but not required as long as component concentrations can be matched. Alternatively, you can use the run-off buffer from the final size exclusion chromatography step.

    Buffer composition: most buffer solutions (pH 4-10) with or without salt at typical physiological concentrations should be adequate. If you have the choice between high salt and low salt buffer use the one with lower salt concentration, unless your protein is better soluble at the higher salt concentration. Using glycerol up to 5% is OK, but make sure you have the exact matching buffer for the background subtraction. Avoid detergents! Please bring at least several ml of buffer solution.

    Optional items: Sulfur-reducing agents such as DTT, TCEP, and 2-mercaptoethanol often protect proteins from excessive radiation damage. If your protein tolerates, use one of them at 1-5mM. The use of glycerol or lower/higher salt concentration may help maintain sample monodispersity.

     

    Crystallography Sample Preparation and General Guidelines

    For those of you planning on sending in crystals to SSRL, please refer to the instructions found HERE. This provides information on acceptable pin types and best practices to optimize the process.

    Our final deadline for receiving samples at SSRL is January 17th. Please be sure that they arrive before this date and that SSRL is notified of the shipment

     

     

     

Grant Writing Workshop

 

Grant Writers' Seminars and Workshops (GWSW) and BioXFEL are hosting a one-day grant writing workshop prior to the 2020 BioXFEL Annual International Conference on Monday, January 27th. John D. Robertson, PhD from GWSW will present "Write Winning Grant Proposals" to attendees interested in learning more about submitting proposals to NIH or NSF. The workshop will cover the essential strategies to writing a winning NIH and NSF proposal, includes one of four workbooks (described below) and a digital copy of the presentation. This event is free of charge for all BioXFEL members, however a portion of the costs will be charged to outside participants. More information on payment can be found on the conference website form.

Read more...

Structural Biology with X-rays: Data Collection and Analysis at the SSRL Synchrotron

BioXFEL will be sponsoring a X-ray Data Collection and Data Analysis workshop in collaboration with scientists at the Stanford Linear Accelerator Center (SLAC) National Lab on Saturday and Sunday January 25th - 26th (and optionally, on Monday the 27th for additional hands-on instruction). We will be offering a hands-on training workshop for protein crystallography, small angle X-ray scattering, and x-ray spectroscopy and imaging with remote access to the synchrotron at SSRL for data collection and data analysis. The workshop will first provide participants with a fundamental overview of the data collection process. This will be followed by practical sessions in sample handling, data collection strategies and logistics that are necessary to collect and process X-ray data from macromolecular crystals, samples in solution and include spectroscopy and imaging examples from a board variety of biological and environmental examples. Students are encouraged to send in either protein crystal samples or solution scattering samples – please contact the workshop organizers if you are interested or if you have any questions.

Read more...