title: Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns.
abstract: Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of the Computational Crystallography Toolbox (cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.
authors: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Aaron S
authors: AS
authors: Brewster
authors: UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095-1570, USA.
authors: Michael R
authors: MR
authors: Sawaya
authors: UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095-1570, USA.
authors: Jose
authors: J
authors: Rodriguez
authors: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Johan
authors: J
authors: Hattne
authors: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Nathaniel
authors: N
authors: Echols
authors: UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095-1570, USA.
authors: Heather T
authors: HT
authors: McFarlane
authors: UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095-1570, USA.
authors: Duilio
authors: D
authors: Cascio
authors: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Paul D
authors: PD
authors: Adams
authors: UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095-1570, USA.
authors: David S
authors: DS
authors: Eisenberg
authors: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors: Nicholas K
authors: NK
authors: Sauter
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D058227:Amyloidogenic Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray / Q000191:economics / Q000379:methods*; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*
chemical_list: D058227:Amyloidogenic Proteins; D010455:Peptides
keywords: Sup35 yeast prion; XFEL; crystallography; indexing methods