TY - JOUR
T1 - SPIND
T2 - A reference-based auto-indexing algorithm for sparse serial crystallography data
AU - Li, Chufeng
AU - Li, Xuanxuan
AU - Kirian, Richard
AU - Spence, John
AU - Liu, Haiguang
AU - Zatsepin, Nadia
N1 - Funding Information:
We thank the group of Weontae Lee and Jihye Yun at the Department of Biochemistry in Yonsei University, Seoul, for providing the CIR SFX data set for this study, collected at the LCLS, SLAC National Accelerator Laboratory.
Funding Information:
This work is supported by the STC Program of the National Science Foundation through BioXFEL under Agreement No. 1231306, ABI Innovation: New Algorithms for Biological X-ray Free Electron Laser Data under NSF grant No. 1565180, and the National Natural Science Foundation of China (awarded to H. Liu) #11575021, U1530401, and U1430237. Use of the LCLS at the SLAC National Accelerator Laboratory is supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under contract No. DE-AC02-76SF00515.
Publisher Copyright:
© 2019.
PY - 2019
Y1 - 2019
N2 - SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns ('stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008), Acta Cryst. E64, o1286], which is challenging for commonly used indexing algorithms. SPIND, integrated with CrystFEL [White et al. (2012), J. Appl. Cryst. 45, 335-341], is then shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2 and the NTQ chloride-pumping rhodopsin (CIR). The study demonstrates the suitability of SPIND for indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets. SPIND is written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND.
AB - SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns ('stills') that requires the positions of only five Bragg peaks in a single pattern, when provided with unit-cell parameters. The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns using simulated data from microcrystals of a small inorganic molecule containing three iodines, 5-amino-2,4,6-triiodoisophthalic acid monohydrate (I3C) [Beck & Sheldrick (2008), Acta Cryst. E64, o1286], which is challenging for commonly used indexing algorithms. SPIND, integrated with CrystFEL [White et al. (2012), J. Appl. Cryst. 45, 335-341], is then shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2 and the NTQ chloride-pumping rhodopsin (CIR). The study demonstrates the suitability of SPIND for indexing sparse inorganic crystal data with smaller unit cells, and for improving the quality of serial femtosecond protein crystallography data, significantly reducing the amount of sample and beam time required by making better use of limited data sets. SPIND is written in Python and is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND.
KW - Auto-indexing algorithms
KW - Bragg peaks
KW - Diffract-then-destroy
KW - Dynamical studies
KW - Electron diffraction
KW - Serial crystallography
KW - X-ray free-electron lasers
KW - XFEL
UR - http://www.scopus.com/inward/record.url?scp=85059914366&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85059914366&partnerID=8YFLogxK
U2 - 10.1107/S2052252518014951
DO - 10.1107/S2052252518014951
M3 - Article
AN - SCOPUS:85059914366
SN - 2052-2525
VL - 6
SP - 72
EP - 84
JO - IUCrJ
JF - IUCrJ
ER -