Search Results - "Holton, James"

Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures by de la Mora, Eugenio, Coquelle, Nicolas, Bury, Charles S., Rosenthal, Martin, Holton, James M., Carmichael, Ian, Garman, Elspeth F., Burghammer, Manfred, Colletier, Jacques-Philippe, Weik, Martin

“…Radiation damage limits the accuracy of macromolecular structures in X-ray crystallography. Cryogenic (cryo-) cooling reduces the global radiation damage rate…”
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A beginner's guide to radiation damage by Holton, James M.

“…Many advances in the understanding of radiation damage to protein crystals, particularly at cryogenic temperatures, have been made in recent years, but with…”
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Large language models generate functional protein sequences across diverse families by Madani, Ali, Krause, Ben, Greene, Eric R., Subramanian, Subu, Mohr, Benjamin P., Holton, James M., Olmos, Jose Luis, Xiong, Caiming, Sun, Zachary Z., Socher, Richard, Fraser, James S., Naik, Nikhil

“…Deep-learning language models have shown promise in various biotechnological applications, including protein design and engineering. Here we describe ProGen, a…”
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Challenge data set for macromolecular multi‐microcrystallography by Holton, James M.

“…A synthetic data set demonstrating a particularly challenging case of indexing ambiguity in the context of radiation damage was generated. This set shall serve…”
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Accessing protein conformational ensembles using room-temperature X-ray crystallography by Fraser, James S, van den Bedem, Henry, Samelson, Avi J, Lang, P. Therese, Holton, James M, Echols, Nathaniel, Alber, Tom

“…Modern protein crystal structures are based nearly exclusively on X-ray data collected at cryogenic temperatures (generally 100 K). The cooling process is…”
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Structures of two novel crystal forms of Aspergillus oryzae alpha amylase (taka-amylase) by Gee, Christine L., Holton, James M., McPherson, Alexander

“…The structures of Aspergillus oryzae α-amylase were determined in a tetragonal crystal, having one molecule as asymmetric unit, and a monoclinic crystal with…”
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Guide-bound structures of an RNA-targeting A-cleaving CRISPR–Cas13a enzyme by Knott, Gavin J, East-Seletsky, Alexandra, Cofsky, Joshua C, Holton, James M, Charles, Emeric, O'Connell, Mitchell R, Doudna, Jennifer A

“…Crystal structures of unprocessed and mature crRNA-bound LbaCas13a shed light upon catalytic residues involved in crRNA maturation and mechanisms blocking…”
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The minimum crystal size needed for a complete diffraction data set by Holton, James M., Frankel, Kenneth A.

“…In this work, classic intensity formulae were united with an empirical spot‐fading model in order to calculate the diameter of a spherical crystal that will…”
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Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition by Hussein, Rana, Ibrahim, Mohamed, Bhowmick, Asmit, Simon, Philipp S., Chatterjee, Ruchira, Lassalle, Louise, Doyle, Margaret, Bogacz, Isabel, Kim, In-Sik, Cheah, Mun Hon, Gul, Sheraz, de Lichtenberg, Casper, Chernev, Petko, Pham, Cindy C., Young, Iris D., Carbajo, Sergio, Fuller, Franklin D., Alonso-Mori, Roberto, Batyuk, Alex, Sutherlin, Kyle D., Brewster, Aaron S., Bolotovsky, Robert, Mendez, Derek, Holton, James M., Moriarty, Nigel W., Adams, Paul D., Bergmann, Uwe, Sauter, Nicholas K., Dobbek, Holger, Messinger, Johannes, Zouni, Athina, Kern, Jan, Yachandra, Vittal K., Yano, Junko

“…Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron,…”
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Untangling the sequence of events during the S₂ → S₃ transition in photosystem II and implications for the water oxidation mechanism by Ibrahim, Mohamed, Fransson, Thomas, Chatterjee, Ruchira, Cheah, Mun Hon, Hussein, Rana, Lassalle, Louise, Sutherlin, Kyle D., Young, Iris D., Fuller, Franklin D., Gul, Sheraz, Kim, In-Sik, Simon, Philipp S., de Lichtenberg, Casper, Chernev, Petko, Bogacz, Isabel, Pham, Cindy C., Orville, Allen M., Saichek, Nicholas, Northen, Trent, Batyuk, Alexander, Carbajo, Sergio, Alonso-Mori, Roberto, Tono, Kensuke, Owada, Shigeki, Bhowmick, Asmit, Bolotovsky, Robert, Mendez, Derek, Moriarty, Nigel W., Holton, James M., Dobbek, Holger, Brewster, Aaron S., Adams, Paul D., Sauter, Nicholas K., Bergmann, Uwe, Zouni, Athina, Messinger, Johannes, Kern, Jan, Yachandra, Vittal K., Yano, Junko

“…In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II)…”
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Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism by Ibrahim, Mohamed, Fransson, Thomas, Chatterjee, Ruchira, Cheah, Mun Hon, Hussein, Rana, Lassalle, Louise, Sutherlin, Kyle D, Young, Iris D, Fuller, Franklin D, Gul, Sheraz, Kim, In-Sik, Simon, Philipp S, de Lichtenberg, Casper, Chernev, Petko, Bogacz, Isabel, Pham, Cindy C, Orville, Allen M, Saichek, Nicholas, Northen, Trent, Batyuk, Alexander, Carbajo, Sergio, Alonso-Mori, Roberto, Tono, Kensuke, Owada, Shigeki, Bhowmick, Asmit, Bolotovsky, Robert, Mendez, Derek, Moriarty, Nigel W, Holton, James M, Dobbek, Holger, Brewster, Aaron S, Adams, Paul D, Sauter, Nicholas K, Bergmann, Uwe, Zouni, Athina, Messinger, Johannes, Kern, Jan, Yachandra, Vittal K, Yano, Junko

“…In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II)…”
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Towards the spatial resolution of metalloprotein charge states by detailed modeling of XFEL crystallographic diffraction by Sauter, Nicholas K., Kern, Jan, Yano, Junko, Holton, James M.

“…Oxidation states of individual metal atoms within a metalloprotein can be assigned by examining X‐ray absorption edges, which shift to higher energy for…”
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R‐factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures by Holton, James M, Classen, Scott, Frankel, Kenneth A, Tainer, John A

“…In macromolecular crystallography, the agreement between observed and predicted structure factors (Rcᵣyₛₜ and Rfᵣₑₑ) is seldom better than 20%. This is much…”
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Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source by 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.

“…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…”
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Structural evidence for intermediates during O2 formation in photosystem II by Bhowmick, Asmit, Hussein, Rana, Bogacz, Isabel, Simon, Philipp S., Ibrahim, Mohamed, Chatterjee, Ruchira, Doyle, Margaret D., Cheah, Mun Hon, Fransson, Thomas, Chernev, Petko, Kim, In-Sik, Makita, Hiroki, Dasgupta, Medhanjali, Kaminsky, Corey J., Zhang, Miao, Gätcke, Julia, Haupt, Stephanie, Nangca, Isabela I., Keable, Stephen M., Aydin, A. Orkun, Tono, Kensuke, Owada, Shigeki, Gee, Leland B., Fuller, Franklin D., Batyuk, Alexander, Alonso-Mori, Roberto, Holton, James M., Paley, Daniel W., Moriarty, Nigel W., Mamedov, Fikret, Adams, Paul D., Brewster, Aaron S., Dobbek, Holger, Sauter, Nicholas K., Bergmann, Uwe, Zouni, Athina, Messinger, Johannes, Kern, Jan, Yano, Junko, Yachandra, Vittal K.

“…In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical…”
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Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite by Bruning, John M, Wang, Yan, Oltrabella, Francesca, Tian, Boxue, Kholodar, Svetlana A, Liu, Harrison, Bhattacharya, Paulomi, Guo, Su, Holton, James M, Fletterick, Robert J, Jacobson, Matthew P, England, Pamela M

“…Nurr1, a nuclear receptor essential for the development, maintenance, and survival of midbrain dopaminergic neurons, is a potential therapeutic target for…”
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Influence of pump laser fluence on ultrafast myoglobin structural dynamics by Barends, Thomas R. M., Gorel, Alexander, Bhattacharyya, Swarnendu, Schirò, Giorgio, Bacellar, Camila, Cirelli, Claudio, Colletier, Jacques-Philippe, Foucar, Lutz, Grünbein, Marie Luise, Hartmann, Elisabeth, Hilpert, Mario, Holton, James M., Johnson, Philip J. M., Kloos, Marco, Knopp, Gregor, Marekha, Bogdan, Nass, Karol, Nass Kovacs, Gabriela, Ozerov, Dmitry, Stricker, Miriam, Weik, Martin, Doak, R. Bruce, Shoeman, Robert L., Milne, Christopher J., Huix-Rotllant, Miquel, Cammarata, Marco, Schlichting, Ilme

“…High-intensity femtosecond pulses from an X-ray free-electron laser enable pump–probe experiments for the investigation of electronic and nuclear changes…”
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Protein structural ensembles are revealed by redefining X-ray electron density noise by Lang, P. Therese, Holton, James M., Fraser, James S., Alber, Tom

“…To increase the power of X-ray crystallography to determine not only the structures but also the motions of biomolecules, we developed methods to address two…”
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Predicting the X-ray lifetime of protein crystals by Zeldin, Oliver B., Brockhauser, Sandor, Bremridge, John, Holton, James M., Garman, Elspeth F.

“…Radiation damage is a major cause of failure in macromolecular crystallography experiments. Although it is always best to evenly illuminate the entire volume…”
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Structures of the Bacterial Ribosome at 3.5 Å Resolution by Schuwirth, Barbara S., Borovinskaya, Maria A., Hau, Cathy W., Zhang, Wen, Vila-Sanjurjo, Antón, Holton, James M., Jamie H. Doudna Cate

“…We describe two structures of the intact bacterial ribosome from Escherichia coli determined to a resolution of 3.5 angstroms by x-ray crystallography. These…”
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