Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source

Classen, Scott; Hura, Greg L.; Holton, James M.; Rambo, Robert P.; Rodic, Ivan; McGuire, Patrick J.; Dyer, Kevin; Hammel, Michal; Meigs, George; Frankel, Kenneth A.; Tainer, John A.

doi:10.1107/s0021889812048698

Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source

Journal Article · Thu Jan 17 00:00:00 EST 2013 · Journal of Applied Crystallography

DOI:https://doi.org/10.1107/s0021889812048698· OSTI ID:1625650

Classen, Scott ^[1]; Hura, Greg L. ^[2]; Holton, James M. ^[3]; Rambo, Robert P. ^[2]; Rodic, Ivan ^[4]; McGuire, Patrick J. ^[2]; Dyer, Kevin ^[2]; Hammel, Michal ^[2]; Meigs, George ^[2]; Frankel, Kenneth A. ^[5]; Tainer, John A. ^[4]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Bioscience Division; DOE/OSTI
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Bioscience Division
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Bioscience Division; Univ. of California, San Francisco, CA (United States). Dept. of Biochemistry and Biophysics
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Sciences Division
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Engineering Division

The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world's mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B₄C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625650

Journal Information:: Journal of Applied Crystallography, Journal Name: Journal of Applied Crystallography Journal Issue: 1 Vol. 46; ISSN 0021-8898

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

References (76)

Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law Rambo, Robert P.; Tainer, John A. Biopolymers, Vol. 95, Issue 8 https://doi.org/10.1002/bip.21638	journal	April 2011
ALS Mutants of Human Superoxide Dismutase Form Fibrous Aggregates Via Framework Destabilization DiDonato, Michael; Craig, Lisa; Huff, Mary E. Journal of Molecular Biology, Vol. 332, Issue 3 https://doi.org/10.1016/S0022-2836(03)00889-1	journal	September 2003
The structural biochemistry of the superoxide dismutases Perry, J. J. P.; Shin, D. S.; Getzoff, E. D. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1804, Issue 2 https://doi.org/10.1016/j.bbapap.2009.11.004	journal	February 2010
Structure of the Autoinhibited Kinase Domain of CaMKII and SAXS Analysis of the Holoenzyme Rosenberg, Oren S.; Deindl, Sebastian; Sung, Rou-Jia Cell, Vol. 123, Issue 5 https://doi.org/10.1016/j.cell.2005.10.029	journal	December 2005
XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations Fan, Li; Fuss, Jill O.; Cheng, Quen J. Cell, Vol. 133, Issue 5 https://doi.org/10.1016/j.cell.2008.04.030	journal	May 2008
Mre11 Dimers Coordinate DNA End Bridging and Nuclease Processing in Double-Strand-Break Repair Williams, R. Scott; Moncalian, Gabriel; Williams, Jessica S. Cell, Vol. 135, Issue 1 https://doi.org/10.1016/j.cell.2008.08.017	journal	October 2008
Nbs1 Flexibly Tethers Ctp1 and Mre11-Rad50 to Coordinate DNA Double-Strand Break Processing and Repair Williams, R. Scott; Dodson, Gerald E.; Limbo, Oliver Cell, Vol. 139, Issue 1 https://doi.org/10.1016/j.cell.2009.07.033	journal	October 2009
Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily Tsutakawa, Susan E.; Classen, Scott; Chapados, Brian R. Cell, Vol. 145, Issue 2 https://doi.org/10.1016/j.cell.2011.03.004	journal	April 2011
The intricate structural chemistry of base excision repair machinery: Implications for DNA damage recognition, removal, and repair Hitomi, Kenichi; Iwai, Shigenori; Tainer, John A. DNA Repair, Vol. 6, Issue 4 https://doi.org/10.1016/j.dnarep.2006.10.004	journal	April 2007
Mre11–Rad50–Nbs1 conformations and the control of sensing, signaling, and effector responses at DNA double-strand breaks Williams, Gareth J.; Lees-Miller, Susan P.; Tainer, John A. DNA Repair, Vol. 9, Issue 12 https://doi.org/10.1016/j.dnarep.2010.10.001	journal	December 2010
XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase Fuss, Jill O.; Tainer, John A. DNA Repair, Vol. 10, Issue 7 https://doi.org/10.1016/j.dnarep.2011.04.028	journal	July 2011
Superoxide Dismutase from the Eukaryotic Thermophile Alvinella pompejana: Structures, Stability, Mechanism, and Insights into Amyotrophic Lateral Sclerosis Shin, David S.; DiDonato, Michael; Barondeau, David P. Journal of Molecular Biology, Vol. 385, Issue 5 https://doi.org/10.1016/j.jmb.2008.11.031	journal	February 2009
A Flexible Interface between DNA Ligase and PCNA Supports Conformational Switching and Efficient Ligation of DNA Pascal, John M.; Tsodikov, Oleg V.; Hura, Greg L. Molecular Cell, Vol. 24, Issue 2 https://doi.org/10.1016/j.molcel.2006.08.015	journal	October 2006
Automated Sample Mounting and Alignment System for Biological Crystallography at a Synchrotron Source Snell, Gyorgy; Cork, Carl; Nordmeyer, Robert Structure, Vol. 12, Issue 4 https://doi.org/10.1016/j.str.2004.03.011	journal	April 2004
The Structure of the MAP2K MEK6 Reveals an Autoinhibitory Dimer Min, Xiaoshan; Akella, Radha; He, Haixia Structure, Vol. 17, Issue 1 https://doi.org/10.1016/j.str.2008.11.007	journal	January 2009
Crystal and Solution Structures of a Prokaryotic M16B Peptidase: an Open and Shut Case Aleshin, Alexander E.; Gramatikova, Svetlana; Hura, Gregory L. Structure, Vol. 17, Issue 11 https://doi.org/10.1016/j.str.2009.09.009	journal	November 2009
XLF Regulates Filament Architecture of the XRCC4·Ligase IV Complex Hammel, Michal; Yu, Yaping; Fang, Shujuan Structure, Vol. 18, Issue 11 https://doi.org/10.1016/j.str.2010.09.009	journal	November 2010
Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases Grasby, Jane A.; Finger, L. David; Tsutakawa, Susan E. Trends in Biochemical Sciences, Vol. 37, Issue 2 https://doi.org/10.1016/j.tibs.2011.10.003	journal	February 2012
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution Putnam, Christopher D.; Hammel, Michal; Hura, Greg L. Quarterly Reviews of Biophysics, Vol. 40, Issue 3 https://doi.org/10.1017/S0033583507004635	journal	August 2007
Crystallographic Structures of Discosoma Red Fluorescent Protein with Immature and Mature Chromophores: Linking Peptide Bond Trans−Cis Isomerization and Acylimine Formation in Chromophore Maturation ^† ^, ^‡ Tubbs, Julie L.; Tainer, John A.; Getzoff, Elizabeth D. Biochemistry, Vol. 44, Issue 29 https://doi.org/10.1021/bi0472907	journal	July 2005
Nickel Superoxide Dismutase Structure and Mechanism ^† Barondeau, David P.; Kassmann, Carey J.; Bruns, Cami K. Biochemistry, Vol. 43, Issue 25 https://doi.org/10.1021/bi0496081	journal	June 2004
Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching between Two DNA-Bound States Cotner-Gohara, Elizabeth; Kim, In-Kwon; Hammel, Michal Biochemistry, Vol. 49, Issue 29 https://doi.org/10.1021/bi100503w	journal	July 2010
Structural Dynamics and Single-Stranded DNA Binding Activity of the Three N-Terminal Domains of the Large Subunit of Replication Protein A from Small Angle X-ray Scattering Pretto, Dalyir I.; Tsutakawa, Susan; Brosey, Chris A. Biochemistry, Vol. 49, Issue 13 https://doi.org/10.1021/bi9019934	journal	April 2010
Structural Evidence for an Enolate Intermediate in GFP Fluorophore Biosynthesis Barondeau, David P.; Tainer, John A.; Getzoff, Elizabeth D. Journal of the American Chemical Society, Vol. 128, Issue 10 https://doi.org/10.1021/ja0552693	journal	March 2006
Understanding GFP Posttranslational Chemistry: Structures of Designed Variants that Achieve Backbone Fragmentation, Hydrolysis, and Decarboxylation Barondeau, David P.; Kassmann, Carey J.; Tainer, John A. Journal of the American Chemical Society, Vol. 128, Issue 14 https://doi.org/10.1021/ja056635l	journal	April 2006
Recognition of the Ring-Opened State of Proliferating Cell Nuclear Antigen by Replication Factor C Promotes Eukaryotic Clamp-Loading Tainer, John A.; McCammon, J. Andrew; Ivanov, Ivaylo Journal of the American Chemical Society, Vol. 132, Issue 21 https://doi.org/10.1021/ja100365x	journal	June 2010
γH2A binds Brc1 to maintain genome integrity during S-phase Williams, Jessica S.; Williams, R. Scott; Dovey, Claire L. The EMBO Journal, Vol. 29, Issue 6 https://doi.org/10.1038/emboj.2009.413	journal	January 2010
Flipping of alkylated DNA damage bridges base and nucleotide excision repair Tubbs, Julie L.; Latypov, Vitaly; Kanugula, Sreenivas Nature, Vol. 459, Issue 7248 https://doi.org/10.1038/nature08076	journal	June 2009
Microbial metalloproteomes are largely uncharacterized Cvetkovic, Aleksandar; Menon, Angeli Lal; Thorgersen, Michael P. Nature, Vol. 466, Issue 7307 https://doi.org/10.1038/nature09265	journal	July 2010
Cancer, cadmium and genome integrity McMurray, Cynthia T.; Tainer, John A. Nature Genetics, Vol. 34, Issue 3 https://doi.org/10.1038/ng0703-239	journal	July 2003
Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS) Hura, Greg L.; Menon, Angeli L.; Hammel, Michal Nature Methods, Vol. 6, Issue 8 https://doi.org/10.1038/nmeth.1353	journal	July 2009
First lasing and operation of an ångstrom-wavelength free-electron laser Emma, P.; Akre, R.; Arthur, J. Nature Photonics, Vol. 4, Issue 9 https://doi.org/10.1038/nphoton.2010.176	journal	August 2010
DNA apurinic-apyrimidinic site binding and excision by endonuclease IV Garcin, Elsa D.; Hosfield, David J.; Desai, Sunil A. Nature Structural & Molecular Biology, Vol. 15, Issue 5 https://doi.org/10.1038/nsmb.1414	journal	April 2008
Molecular mimicry of SUMO promotes DNA repair Prudden, John; Perry, J. Jefferson P.; Arvai, Andrew S. Nature Structural & Molecular Biology, Vol. 16, Issue 5 https://doi.org/10.1038/nsmb.1582	journal	April 2009
ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair Williams, Gareth J.; Williams, R. Scott; Williams, Jessica S. Nature Structural & Molecular Biology, Vol. 18, Issue 4 https://doi.org/10.1038/nsmb.2038	journal	March 2011
Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element Kim, In-Kwon; Kiefer, James R.; Ho, Chris M. W. Nature Structural & Molecular Biology, Vol. 19, Issue 6 https://doi.org/10.1038/nsmb.2305	journal	May 2012
SPRTN protease-cleaved MRE11 decreases DNA repair and radiosensitises cancer cells Na, Juri; Newman, Joseph A.; Then, Chee Kin Cell Death & Disease, Vol. 12, Issue 2 https://doi.org/10.1038/s41419-021-03437-w	journal	February 2021
Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism Yamagata, Atsushi; Tainer, John A. The EMBO Journal, Vol. 26, Issue 3 https://doi.org/10.1038/sj.emboj.7601544	journal	January 2007
Archaeal flagellar ATPase motor shows ATP-dependent hexameric assembly and activity stimulation by specific lipid binding Ghosh, Abhrajyoti; Hartung, Sophia; van der Does, Chris Biochemical Journal, Vol. 437, Issue 1, p. 43-52 https://doi.org/10.1042/BJ20110410	journal	July 2011
Experimental determination of the radiation dose limit for cryocooled protein crystals Owen, R. L.; Rudino-Pinera, E.; Garman, E. F. Proceedings of the National Academy of Sciences, Vol. 103, Issue 13 https://doi.org/10.1073/pnas.0600973103	journal	March 2006
Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV Ivanov, I.; Tainer, J. A.; McCammon, J. A. Proceedings of the National Academy of Sciences, Vol. 104, Issue 5 https://doi.org/10.1073/pnas.0603468104	journal	January 2007
Small-angle scattering and the structure of ambient liquid water Clark, G. N. I.; Hura, G. L.; Teixeira, J. Proceedings of the National Academy of Sciences, Vol. 107, Issue 32 https://doi.org/10.1073/pnas.1006599107	journal	July 2010
Conformational trapping of Mismatch Recognition Complex MSH2/MSH3 on repair-resistant DNA loops Lang, W. H.; Coats, J. E.; Majka, J. Proceedings of the National Academy of Sciences, Vol. 108, Issue 42 https://doi.org/10.1073/pnas.1105461108	journal	September 2011
Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA Tsutakawa, S. E.; Van Wynsberghe, A. W.; Freudenthal, B. D. Proceedings of the National Academy of Sciences, Vol. 108, Issue 43 https://doi.org/10.1073/pnas.1110480108	journal	October 2011
Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability Querol-Audi, J.; Yan, C.; Xu, X. Proceedings of the National Academy of Sciences, Vol. 109, Issue 22 https://doi.org/10.1073/pnas.1121116109	journal	May 2012
Ku and DNA-dependent Protein Kinase Dynamic Conformations and Assembly Regulate DNA Binding and the Initial Non-homologous End Joining Complex Hammel, Michal; Yu, Yaping; Mahaney, Brandi L. Journal of Biological Chemistry, Vol. 285, Issue 2 https://doi.org/10.1074/jbc.M109.065615	journal	November 2009
XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair Hammel, Michal; Rey, Martial; Yu, Yaping Journal of Biological Chemistry, Vol. 286, Issue 37 https://doi.org/10.1074/jbc.M111.272641	journal	July 2011
Structural Tuning of the Fluorescent Protein iLOV for Improved Photostability Christie, John M.; Hitomi, Kenichi; Arvai, Andrew S. Journal of Biological Chemistry, Vol. 287, Issue 26 https://doi.org/10.1074/jbc.M111.318881	journal	May 2012
Amino Acid Substitution at the Dimeric Interface of Human Manganese Superoxide Dismutase Hearn, Amy S.; Fan, Li; Lepock, James R. Journal of Biological Chemistry, Vol. 279, Issue 7 https://doi.org/10.1074/jbc.M311310200	journal	February 2004
The Protein Data Bank Berman, H. M. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.235	journal	January 2000
Mapping interactions between the RNA chaperone FinO and its RNA targets Arthur, David C.; Edwards, Ross A.; Tsutakawa, Susan Nucleic Acids Research, Vol. 39, Issue 10 https://doi.org/10.1093/nar/gkr025	journal	January 2011
An automated system to mount cryo-cooled protein crystals on a synchrotron beamline, using compact sample cassettes and a small-scale robot Cohen, Aina E.; Ellis, Paul J.; Miller, Mitchell D. Journal of Applied Crystallography, Vol. 35, Issue 6 https://doi.org/10.1107/S0021889802016709	journal	November 2002
Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33 Round, A. R.; Franke, D.; Moritz, S. Journal of Applied Crystallography, Vol. 41, Issue 5 https://doi.org/10.1107/S0021889808021018	journal	August 2008
Scatterless hybrid metal–single-crystal slit for small-angle X-ray scattering and high-resolution X-ray diffraction Li, Youli; Beck, Roy; Huang, Tuo Journal of Applied Crystallography, Vol. 41, Issue 6 https://doi.org/10.1107/S0021889808031129	journal	November 2008
Combined sampler robot and high-performance liquid chromatography: a fully automated system for biological small-angle X-ray scattering experiments at the Synchrotron SOLEIL SWING beamline David, G.; Pérez, J. Journal of Applied Crystallography, Vol. 42, Issue 5 https://doi.org/10.1107/S0021889809029288	journal	September 2009
Remote access to crystallography beamlines at SSRL: novel tools for training, education and collaboration Smith, Clyde A.; Card, Graeme L.; Cohen, Aina E. Journal of Applied Crystallography, Vol. 43, Issue 5 https://doi.org/10.1107/S0021889810024696	journal	August 2010
Upgrade of automated sample exchanger SPACE Murakami, Hironori; Ueno, Go; Shimizu, Nobutaka Journal of Applied Crystallography, Vol. 45, Issue 2 https://doi.org/10.1107/S0021889812003585	journal	March 2012
Instrumental setup for high-throughput small- and wide-angle solution scattering at the X33 beamline of EMBL Hamburg Blanchet, Clement E.; Zozulya, Alexey V.; Kikhney, Alexey G. Journal of Applied Crystallography, Vol. 45, Issue 3 https://doi.org/10.1107/S0021889812013490	journal	May 2012
Automated mounting, centering and screening of crystals for high-throughput protein crystallography Karain, W. I.; Bourenkov, G. P.; Blume, H. Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 10 https://doi.org/10.1107/S0907444902012751	journal	September 2002
Unravelling the structural chemistry of the colouration mechanism in lobster shell Chayen, Naomi E.; Cianci, Michele; Grossmann, J. Günter Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 12 https://doi.org/10.1107/S0907444903025952	journal	November 2003
Advanced beamline automation for biological crystallography experiments Cork, Carl; O'Neill, James; Taylor, John Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8 https://doi.org/10.1107/S0907444906014120	journal	July 2006
Automation of sample mounting for macromolecular crystallography Cipriani, F.; Felisaz, F.; Launer, L. Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 10 https://doi.org/10.1107/S0907444906030587	journal	September 2006
A 7 µm mini-beam improves diffraction data from small or imperfect crystals of macromolecules Sanishvili, Ruslan; Nagarajan, Venugopalan; Yoder, Derek Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 4 https://doi.org/10.1107/S0907444908001741	journal	March 2008
New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection Soltis, S. Michael; Cohen, Aina E.; Deacon, Ashley Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 12 https://doi.org/10.1107/S0907444908030564	journal	November 2008
The minimum crystal size needed for a complete diffraction data set Holton, James M.; Frankel, Kenneth A. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007262	journal	March 2010
Blu-Ice and the Distributed Control System : software for data acquisition and instrument control at macromolecular crystallography beamlines McPhillips, Timothy M.; McPhillips, Scott E.; Chiu, Hsiu-Ju Journal of Synchrotron Radiation, Vol. 9, Issue 6 https://doi.org/10.1107/S0909049502015170	journal	November 2002
Suite of three protein crystallography beamlines with single superconducting bend magnet as the source MacDowell, Alastair A.; Celestre, Rich S.; Howells, Malcolm Journal of Synchrotron Radiation, Vol. 11, Issue 6 https://doi.org/10.1107/S0909049504024835	journal	October 2004
Upgrade of the CATS sample changer on FIP-BM30A at the ESRF: towards a commercialized standard Jacquamet, L.; Joly, J.; Bertoni, A. Journal of Synchrotron Radiation, Vol. 16, Issue 1 https://doi.org/10.1107/S0909049508031105	journal	November 2008
A beginner's guide to radiation damage Holton, James M. Journal of Synchrotron Radiation, Vol. 16, Issue 2 https://doi.org/10.1107/S0909049509004361	journal	February 2009
Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice / DCS control system Classen, Scott; Rodic, Ivan; Holton, James Journal of Synchrotron Radiation, Vol. 17, Issue 6 https://doi.org/10.1107/S0909049510028566	journal	September 2010
The Protein Data Bank Berman, Helen M.; Battistuz, Tammy; Bhat, T. N. Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 6 https://doi.org/10.1107/s0907444902003451	journal	May 2002
Structural Mechanism of Abscisic Acid Binding and Signaling by Dimeric PYR1 Nishimura, N.; Hitomi, K.; Arvai, A. S. Science, Vol. 326, Issue 5958 https://doi.org/10.1126/science.1181829	journal	October 2009
Plant UVR8 Photoreceptor Senses UV-B by Tryptophan-Mediated Disruption of Cross-Dimer Salt Bridges Christie, J. M.; Arvai, A. S.; Baxter, K. J. Science, Vol. 335, Issue 6075 https://doi.org/10.1126/science.1218091	journal	February 2012
DNA Repair and Global Sumoylation Are Regulated by Distinct Ubc9 Noncovalent Complexes Prudden, J.; Perry, J. J. P.; Nie, M. Molecular and Cellular Biology, Vol. 31, Issue 11 https://doi.org/10.1128/MCB.05188-11	journal	March 2011
Solution structure of RNase P RNA Kazantsev, A. V.; Rambo, R. P.; Karimpour, S. RNA, Vol. 17, Issue 6 https://doi.org/10.1261/rna.2563511	journal	April 2011
SUMO-Targeted Ubiquitin Ligase, Rad60, and Nse2 SUMO Ligase Suppress Spontaneous Top1–Mediated DNA Damage and Genome Instability Heideker, Johanna; Prudden, John; Perry, J. Jefferson P. PLoS Genetics, Vol. 7, Issue 3 https://doi.org/10.1371/journal.pgen.1001320	journal	March 2011

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A key interaction with RPA orients XPA in NER complexes Topolska-Woś, Agnieszka M.; Sugitani, Norie; Cordoba, John J. Nucleic Acids Research, Vol. 48, Issue 4 https://doi.org/10.1093/nar/gkz1231	journal	January 2020
The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures Holton, James M.; Classen, Scott; Frankel, Kenneth A. The FEBS Journal, Vol. 281, Issue 18 https://doi.org/10.1111/febs.12922	journal	September 2014
Designing and defining dynamic protein cage nanoassemblies in solution Lai, Yen-Ting; Hura, Greg L.; Dyer, Kevin N. Science Advances, Vol. 2, Issue 12 https://doi.org/10.1126/sciadv.1501855	journal	December 2016
HU multimerization shift controls nucleoid compaction Hammel, Michal; Amlanjyoti, Dhar; Reyes, Francis E. Science Advances, Vol. 2, Issue 7 https://doi.org/10.1126/sciadv.1600650	journal	July 2016
Archaeal Genome Guardians Give Insights into Eukaryotic DNA Replication and Damage Response Proteins Shin, David S.; Pratt, Ashley J.; Tainer, John A. Archaea, Vol. 2014 https://doi.org/10.1155/2014/206735	journal	January 2014
Identifying and Visualizing Macromolecular Flexibility in Structural Biology Palamini, Martina; Canciani, Anselmo; Forneris, Federico Frontiers in Molecular Biosciences, Vol. 3 https://doi.org/10.3389/fmolb.2016.00047	journal	September 2016
Small angle x-ray scattering experiments of monodisperse samples close to the solubility limit Martin, Erik W.; Hopkins, Jesse B.; Mittag, Tanja arXiv https://doi.org/10.48550/arxiv.2003.01278	preprint	January 2020
RNA-guided assembly of Rev-RRE nuclear export complexes Bai, Yun; Tambe, Akshay; Zhou, Kaihong eLife, Vol. 3 https://doi.org/10.7554/elife.03656	journal	August 2014
Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a Knott, Gavin J.; Cress, Brady F.; Liu, Jun-Jie eLife, Vol. 8 https://doi.org/10.7554/elife.49110	journal	August 2019
Wedging open a catalytic site Beuve, Annie eLife, Vol. 8 https://doi.org/10.7554/elife.52418	journal	November 2019
Biochemical and structural characterization of two variants of uncertain significance in the PMS2 gene D'Arcy, Brandon M.; Blount, Jessa; Prakash, Aishwarya Human Mutation, Vol. 40, Issue 4 https://doi.org/10.1002/humu.23708	journal	January 2019
Small angle X‐ray scattering‐assisted protein structure prediction in CASP13 and emergence of solution structure differences Hura, Greg L.; Hodge, Curtis D.; Rosenberg, Daniel Proteins: Structure, Function, and Bioinformatics, Vol. 87, Issue 12 https://doi.org/10.1002/prot.25827	journal	August 2019
High-Throughput SAXS for the Characterization of Biomolecules in Solution: A Practical Approach Dyer, Kevin N.; Hammel, Michal; Rambo, Robert P. Structural Genomics https://doi.org/10.1007/978-1-62703-691-7_18	book	October 2013
The role of small-angle scattering in structure-based screening applications Chen, Po-chia; Hennig, Janosch Biophysical Reviews, Vol. 10, Issue 5 https://doi.org/10.1007/s12551-018-0464-x	journal	October 2018
The structure of the periplasmic FlaG–FlaF complex and its essential role for archaellar swimming motility Tsai, Chi-Lin; Tripp, Patrick; Sivabalasarma, Shamphavi Nature Microbiology, Vol. 5, Issue 1 https://doi.org/10.1038/s41564-019-0622-3	journal	December 2019
Aggregation propensities of superoxide dismutase G93 hotspot mutants mirror ALS clinical phenotypes Pratt, A. J.; Shin, D. S.; Merz, G. E. Proceedings of the National Academy of Sciences, Vol. 111, Issue 43 https://doi.org/10.1073/pnas.1308531111	journal	October 2014
Structure of the infectious salmon anemia virus receptor complex illustrates a unique binding strategy for attachment Cook, Jonathan D.; Sultana, Azmiri; Lee, Jeffrey E. Proceedings of the National Academy of Sciences, Vol. 114, Issue 14 https://doi.org/10.1073/pnas.1617993114	journal	March 2017
Structural transition of nanogel star polymers with pH by controlling PEGMA interactions with acid or base copolymers Felberg, Lisa E.; Doshi, Anjali; Hura, Greg L. Molecular Physics, Vol. 114, Issue 21 https://doi.org/10.1080/00268976.2016.1224942	journal	September 2016
Protein Corona Composition and Dynamics on Carbon Nanotubes in Blood Plasma and Cerebrospinal Fluid Pinals, Rebecca L.; Yang, Darwin; Rosenberg, Daniel J. BioRxiv https://doi.org/10.1101/2020.01.13.905356	posted_content	January 2020
Nucleosome scaffolding by Brd4 tandem bromodomains in acetylation-dependent chromatin compartmentalization Olp, Michael D.; Jackson, Vaughn; Smith, Brian C. BioRxiv https://doi.org/10.1101/699967	posted_content	January 2019
Structure-based screening of binding affinities via small-angle X-ray scattering Chen, P.; Masiewicz, P.; Perez, K. https://doi.org/10.1101/715193	posted_content	July 2019
Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy Horst, Benjamin G.; Yokom, Adam L.; Rosenberg, Daniel J. bioRxiv https://doi.org/10.1101/729418	posted_content	August 2019
Structure-based screening of binding affinities via small-angle X-ray scattering Chen, Po-chia; Masiewicz, Pawel; Perez, Kathryn IUCrJ, Vol. 7, Issue 4 https://doi.org/10.1107/S2052252520004169	journal	May 2020
HU multimerization shift controls nucleoid compaction Hammel, Michal; Amlanjyoti, Dhar; Reyes, Francis Acta Crystallographica Section A Foundations and Advances, Vol. 73, Issue a1 https://doi.org/10.1107/s0108767317099019	journal	May 2017
Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility Reimer, Janice; Eivaskhani, Maximilian; Harb, Ingrid Acta Crystallographica Section A Foundations and Advances, Vol. 76, Issue a1 https://doi.org/10.1107/s0108767320098682	journal	August 2020
The accurate assessment of small-angle X-ray scattering data Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G. Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 1 https://doi.org/10.1107/s1399004714010876	journal	January 2015
BioSAXS Sample Changer: a robotic sample changer for rapid and reliable high-throughput X-ray solution scattering experiments Round, Adam; Felisaz, Franck; Fodinger, Lukas Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 1 https://doi.org/10.1107/s1399004714026959	journal	January 2015
ATSAS 2.8 : a comprehensive data analysis suite for small-angle scattering from macromolecular solutions Franke, D.; Petoukhov, M. V.; Konarev, P. V. Journal of Applied Crystallography, Vol. 50, Issue 4 https://doi.org/10.1107/s1600576717007786	journal	June 2017
Smaller capillaries improve the small-angle X-ray scattering signal and sample consumption for biomacromolecular solutions Schroer, Martin A.; Blanchet, Clement E.; Gruzinov, Andrey Yu. Journal of Synchrotron Radiation, Vol. 25, Issue 4 https://doi.org/10.1107/s1600577518007907	journal	June 2018
Investigating increasingly complex macromolecular systems with small-angle X-ray scattering Vestergaard, Bente; Sayers, Zehra IUCrJ, Vol. 1, Issue 6 https://doi.org/10.1107/s2052252514020843	journal	October 2014
De novo design of tunable, pH-driven conformational changes Boyken, Scott E.; Benhaim, Mark A.; Busch, Florian Science, Vol. 364, Issue 6441 https://doi.org/10.1126/science.aav7897	journal	May 2019
Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility Reimer, Janice M.; Eivaskhani, Maximilian; Harb, Ingrid Science, Vol. 366, Issue 6466 https://doi.org/10.1126/science.aaw4388	journal	November 2019
Removal of cesium and strontium radionuclides from aqueous media by sorption onto magnetic potassium zinc hexacyanoferrate(II) Pshinko, G. N.; Puzyrnaya, L. N.; Shunkov, V. S. Radiochemistry, Vol. 58, Issue 5 https://doi.org/10.1134/s1066362216050088	journal	September 2016
From proteomics to discovery of first-in-class ST2 inhibitors active in vivo Ramadan, Abdulraouf M.; Daguindau, Etienne; Rech, Jason C. JCI Insight, Vol. 3, Issue 14 https://doi.org/10.1172/jci.insight.99208	journal	July 2018
Exploring the “minimal” structure of a functional ADAMTS13 by mutagenesis and small-angle X-ray scattering Zhu, Jian; Muia, Joshua; Gupta, Garima Blood, Vol. 133, Issue 17 https://doi.org/10.1182/blood-2018-11-886309	journal	April 2019
Smaller capillaries improve the small-angle X-ray scattering signal and sample consumption for biomacromolecular solutions Schroer, Martin; Blanchet, Clement E.; Gruzinov, Andrey Yu. Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2018-05671	text	January 2018
The role of small-angle scattering in structure-based screening applications Chen, Po-Chia; Hennig, Janosch Deutsches Elektronen-Synchrotron, DESY, Hamburg https://doi.org/10.3204/pubdb-2019-00203	text	January 2018
Structural transition of nanogel star polymers with pH by controlling PEGMA interactions with acid or base copolymers Felberg, Lisa E.; Doshi, Anjali; Hura, Greg L. Figshare https://doi.org/10.6084/m9.figshare.3833526	text	January 2016
Structural transition of nanogel star polymers with pH by controlling PEGMA interactions with acid or base copolymers Felberg, Lisa E.; Doshi, Anjali; Hura, Greg L. Figshare https://doi.org/10.6084/m9.figshare.3833526.v1	text	January 2016
Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy Horst, Benjamin G.; Yokom, Adam L.; Rosenberg, Daniel J. eLife, Vol. 8 https://doi.org/10.7554/elife.50634	journal	September 2019

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