2021 SSRL/LCLS Users Meeting

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Tue Sep 21, 12:00 AM - 7:00 PM PDT / Tue Sep 21, 7:00 AM - Wed Sep 22, 2:00 AM Your local time (19 hours)

B-4: Grow and Behold: Collection and Analysis of XFEL PDB Structure Sample Parameter Data

Luz Alfaro

Grinnell College

Poster Session Link:

https://gather.town/invite?token=0pEoq7VP

ABSTRACT

X-Ray Free Electron Laser crystallography is a relatively new science, with the first

XFEL starting operations in 2009. In experiments using XFELs, an X-ray diffraction light

source provides X-rays that hit crystallized samples, producing diffraction data that is

collected by a high-sensitivity X-ray detector for processing to produce a resolved 3D

structure. The quality of the sample crystals used significantly contributes to the ability

to create a resolved molecular structure. Scientists therefore screen for favorable

crystallization conditions using trials to maximize their chances of making high-quality

crystals. Specific crystallization processes vary from lab to lab and the same holds true

for sample delivery methods. We hypothesize that patterns in the sample parameter

data for reported XFEL protein structures deposited to the Protein Data Bank (PDB)

could reveal best practices for use by scientists new to the field. In this project, we use

data mining of the PDB database to probe these questions.

Upon extracting and analyzing XFEL-sources structures reported in the PDB, we found

that most of the 449 reported XFEL structures had a batch mode crystal growth method.

On the contrary, most of the structures had no data for their reported sample delivery

method, with only 171 structures having a reported delivery method and most of those

being an injection method. To extract more details about the sample delivery method

data, we parsed through 154 papers for the structures that reported DOIs. We found

that structure resolution at XFELs has greatly improved from about 9Å to around 2Å,

which is a level comparable to that achieved by other structure-solving methods.

We conclude that relative to the amount of data obtained on crystal growth methods

from the PDB, there is a lack of reported sample delivery data. We conclude that the

lack of sample parameter details creates a barrier of access to these experimental

methods, and increased details in the PDB would benefit new XFEL users in XFEL

experiment design.

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