Abstract
In recent years, the success of serial femtosecond crystallography and the paucity of beamtime at X-ray free-electron lasers have motivated the development of serial microcrystallography experiments at storage-ring synchrotron sources. However, especially at storage-ring sources, if a crystal is too small it will have suffered significant radiation damage before diffracting a sufficient number of X-rays into Bragg peaks for peak-indexing software to determine the crystal orientation. As a consequence, the data frames of small crystals often cannot be indexed and are discarded. Introduced here is a method based on the expand-maximize-compress (EMC) algorithm to solve protein structures, specifically from data frames for which indexing methods fail because too few X-rays are diffracted into Bragg peaks. The method is demonstrated on a real serial microcrystallography data set whose signals are too weak to be indexed by conventional methods. In spite of the daunting background scatter from the sample-delivery medium, it was still possible to solve the protein structure at 2.1 Å resolution. The ability of the EMC algorithm to analyze weak data frames will help to reduce sample consumption. It will also allow serial microcrystallography to be performed with crystals that are otherwise too small to be feasibly analyzed at storage-ring sources.
| Original language | English |
|---|---|
| Pages (from-to) | 548-558 |
| Number of pages | 11 |
| Journal | IUCrJ |
| Volume | 5 |
| DOIs | |
| Publication status | Published - Jan 1 2018 |
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Keywords
- EMC algorithm
- Protein microcrystallography
- Sparse data
- Storage-ring synchrotron sources
- X-ray serial microcrystallography
ASJC Scopus subject areas
- Chemistry(all)
- Biochemistry
- Materials Science(all)
- Condensed Matter Physics
Cite this
Solving protein structure from sparse serial microcrystal diffraction data at a storage-ring synchrotron source. / Lan, Ti Yen; Wierman, Jennifer L.; Tate, Mark W.; Philipp, Hugh T.; Martin-Garcia, Jose M.; Zhu, Lan; Kissick, David; Fromme, Petra; Fischetti, Robert F.; Liu, Wei; Elser, Veit; Gruner, Sol M.
In: IUCrJ, Vol. 5, 01.01.2018, p. 548-558.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Solving protein structure from sparse serial microcrystal diffraction data at a storage-ring synchrotron source
AU - Lan, Ti Yen
AU - Wierman, Jennifer L.
AU - Tate, Mark W.
AU - Philipp, Hugh T.
AU - Martin-Garcia, Jose M.
AU - Zhu, Lan
AU - Kissick, David
AU - Fromme, Petra
AU - Fischetti, Robert F.
AU - Liu, Wei
AU - Elser, Veit
AU - Gruner, Sol M.
PY - 2018/1/1
Y1 - 2018/1/1
N2 - In recent years, the success of serial femtosecond crystallography and the paucity of beamtime at X-ray free-electron lasers have motivated the development of serial microcrystallography experiments at storage-ring synchrotron sources. However, especially at storage-ring sources, if a crystal is too small it will have suffered significant radiation damage before diffracting a sufficient number of X-rays into Bragg peaks for peak-indexing software to determine the crystal orientation. As a consequence, the data frames of small crystals often cannot be indexed and are discarded. Introduced here is a method based on the expand-maximize-compress (EMC) algorithm to solve protein structures, specifically from data frames for which indexing methods fail because too few X-rays are diffracted into Bragg peaks. The method is demonstrated on a real serial microcrystallography data set whose signals are too weak to be indexed by conventional methods. In spite of the daunting background scatter from the sample-delivery medium, it was still possible to solve the protein structure at 2.1 Å resolution. The ability of the EMC algorithm to analyze weak data frames will help to reduce sample consumption. It will also allow serial microcrystallography to be performed with crystals that are otherwise too small to be feasibly analyzed at storage-ring sources.
AB - In recent years, the success of serial femtosecond crystallography and the paucity of beamtime at X-ray free-electron lasers have motivated the development of serial microcrystallography experiments at storage-ring synchrotron sources. However, especially at storage-ring sources, if a crystal is too small it will have suffered significant radiation damage before diffracting a sufficient number of X-rays into Bragg peaks for peak-indexing software to determine the crystal orientation. As a consequence, the data frames of small crystals often cannot be indexed and are discarded. Introduced here is a method based on the expand-maximize-compress (EMC) algorithm to solve protein structures, specifically from data frames for which indexing methods fail because too few X-rays are diffracted into Bragg peaks. The method is demonstrated on a real serial microcrystallography data set whose signals are too weak to be indexed by conventional methods. In spite of the daunting background scatter from the sample-delivery medium, it was still possible to solve the protein structure at 2.1 Å resolution. The ability of the EMC algorithm to analyze weak data frames will help to reduce sample consumption. It will also allow serial microcrystallography to be performed with crystals that are otherwise too small to be feasibly analyzed at storage-ring sources.
KW - EMC algorithm
KW - Protein microcrystallography
KW - Sparse data
KW - Storage-ring synchrotron sources
KW - X-ray serial microcrystallography
UR - http://www.scopus.com/inward/record.url?scp=85053159147&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85053159147&partnerID=8YFLogxK
U2 - 10.1107/S205225251800903X
DO - 10.1107/S205225251800903X
M3 - Article
VL - 5
SP - 548
EP - 558
JO - IUCrJ
JF - IUCrJ
SN - 2052-2525
ER -