Aaron Brewster Publications

• ExaFEL: extreme-scale real-time data processing for X-ray free electron laser science.
  Blaschke JP, Bolotovsky R, Brewster AS, Donatelli J, DuJardin A, Feng W, Ganapati V, Kroeger W, Mendez D, McCorquodale P, Mirchandaney S, O'Grady CP, Paley DW, Perazzo A, Poitevin FP, Poon BK, Ramakrishnaiah VB, Sauter NK, Shah N, Slaughter E, Sweeney C, Tchoń D, Uervirojnangkoorn M, Wittwer F, Wall ME, Yoon CH, Young ID.
  Frontiers in High Performance Computing 2 (3 Oct 2024)
• Laue-DIALS: Open-source software for polychromatic x-ray diffraction data.
  Hewitt RA, Dalton KM, Mendez DA, Wang HK, Klureza MA, Brookner DE, Greisman JB, McDonagh D, Šrajer V, Sauter NK, Brewster AS, Hekstra DR.
  Struct Dyn 11, 054701. (1 Sep 2024): [PMID:39386198] [Free PMC reprint: PMC11462730]
• 3D Nanocrystallography and the Imperfect Molecular Lattice.
  Vlahakis N, Holton J, Sauter NK, Ercius P, Brewster AS, Rodriguez JA.
  Annual Review of Physical Chemistry 75 , 483-508. (28 Jun 2024)
• Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography.
  Smith N, Dasgupta M, Wych DC, Dolamore C, Sierra RG, Lisova S, Marchany-Rivera D, Cohen AE, Boutet S, Hunter MS, Kupitz C, Poitevin F, Moss FR, Mittan-Moreau DW, Brewster AS, Sauter NK, Young ID, Wolff AM, Tiwari VK, Kumar N, Berkowitz DB, Hadt RG, Thompson MC, Follmer AH, Wall ME, Wilson MA.
  Sci Adv 10, eadk7201. (29 Mar 2024): [PMID:38536910] [Free PMC reprint: PMC10971408]
• Real‐time XFEL data analysis at SLAC and NERSC: A trial run of nascent exascale experimental data analysis.
  Blaschke JP, Brewster AS, Paley DW, Mendez D, Bhowmick A, Sauter NK, Kröger W, Shankar M, Enders B, Bard D.
  Concurrency and Computation: Practice and Experience 36(12):e8019. (13 Feb 2024)

• Engineering Supramolecular Hybrid Architectures with Directional Organofluorine Bonds.
  Kotei PA, Paley DW, Oklejas V, Mittan-Moreau DW, Schriber EA, Aleksich M, Willson MC, Inoue I, Owada S, Tono K, Sugahara M, Inaba-Inoue S, Aquila A, Poitevin F, Blaschke JP, Lisova S, Hunter MS, Sierra RG, Gascón JA, Sauter NK, Brewster AS, Hohman JN.
  Small Science 4, e2300110 (13 Dec 2023).


• In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121.
  Nguyen RC, Davis I, Dasgupta M, Wang Y, Simon PS, Butryn A, Makita H, Bogacz I, Dornevil K, Aller P, Bhowmick A, Chatterjee R, Kim IS, Zhou T, Mendez D, Paley DW, Fuller F, Alonso Mori R, Batyuk A, Sauter NK, Brewster AS, Orville AM, Yachandra VK, Yano J, Kern JF, Liu A.
  J Am Chem Soc 145, 25120-25133. (22 Nov 2023): [PMID:37939223] [Free PMC reprint: PMC10799213]
• Accelerating X-ray tracing for exascale systems using Kokkos.
  Wittwer F, Sauter NK, Mendez D, Poon BK, Brewster AS, Holton JM, Wall ME, Hart WE, Bard DJ, Blaschke JP.
  Concurrency and Computation: Practice and Experience, 36(5):e7944 (02 Nov 2023).
• Going around the Kok cycle of the water oxidation reaction with femtosecond X-ray crystallography.
  Bhowmick A, Simon PS, Bogacz I, Hussein R, Zhang M, Makita H, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Chernev P, Fuller FD, Fransson T, Alonso-Mori R, Brewster AS, Sauter NK, Bergmann U, Dobbek H, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J.
  IUCrJ 10, 642-655. (01 Nov 2023): [PMID:37870936] [Free PMC reprint: PMC10619448]
• Structure of a ribonucleotide reductase R2 protein radical.
  Lebrette H, Srinivas V, John J, Aurelius O, Kumar R, Lundin D, Brewster AS, Bhowmick A, Sirohiwal A, Kim IS, Gul S, Pham C, Sutherlin KD, Simon P, Butryn A, Aller P, Orville AM, Fuller FD, Alonso-Mori R, Batyuk A, Sauter NK, Yachandra VK, Yano J, Kaila VRI, Sjöberg BM, Kern J, Roos K, Högbom M.
  Science 382, 109-113. (06 Oct 2023): [PMID:37797025] [Free PMC reprint: PMC7615503] (SLAC Press release)
• Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography.
  Wolff AM, Nango E, Young ID, Brewster AS, Kubo M, Nomura T, Sugahara M, Owada S, Barad BA, Ito K, Bhowmick A, Carbajo S, Hino T, Holton JM, Im D, O'Riordan LJ, Tanaka T, Tanaka R, Sierra RG, Yumoto F, Tono K, Iwata S, Sauter NK, Fraser JS, Thompson MC.
  Nat Chem 15, 1549-1558. (1 Nov 2023): [PMID:37723259] [Free PMC reprint: PMC10624634]
• Changes in an Enzyme Ensemble During Catalysis Observed by High Resolution XFEL Crystallography.
  Smith N, Dasgupta M, Wych DC, Dolamore C, Sierra RG, Lisova S, Marchany-Rivera D, Cohen AE, Boutet S, Hunter MS, Kupitz C, Poitevin F, Moss FR, Brewster AS, Sauter NK, Young ID, Wolff AM, Tiwari VK, Kumar N, Berkowitz DB, Hadt RG, Thompson MC, Follmer AH, Wall ME, Wilson MA.
  bioRxiv (16 Aug 2023): [PMID:37645800] [Free PMC reprint: PMC10462001]
• XFEL Microcrystallography of Self-Assembling Silver n-Alkanethiolates.
  Aleksich M, Paley DW, Schriber EA, Linthicum W, Oklejas V, Mittan-Moreau DW, Kelly RP, Kotei PA, Ghodsi A, Sierra RG, Aquila A, Poitevin F, Blaschke JP, Vakili M, Milne CJ, Dall'Antonia F, Khakhulin D, Ardana-Lamas F, Lima F, Valerio J, Han H, Gallo T, Yousef H, Turkot O, Bermudez Macias IJ, Kluyver T, Schmidt P, Gelisio L, Round AR, Jiang Y, Vinci D, Uemura Y, Kloos M, Hunter M, Mancuso AP, Huey BD, Parent LR, Sauter NK, Brewster AS, Hohman JN.
  J Am Chem Soc 145, 17042-17055. (09 Aug 2023): [PMID:37524069] (EuXFEL Press release)
• Self-Supervised Deep Learning for Model Correction in the Computational Crystallography Toolbox.
  Ganapati V, Tchon D, Brewster AS, Sauter NK.
  ArXiv (04 Jul 2023): [PMID:37461412] [Free PMC reprint: PMC10350105]
• Structural evidence for intermediates during O₂ formation in photosystem II.
  Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK.
  Nature 617, 629-636. (1 May 2023): [PMID:37138085] [Free PMC reprint: PMC10191843] (LBNL Press release) (SLAC Press release) (SharedIT https://rdcu.be/dbhn2)
• Capturing the sequence of events during the water oxidation reaction in photosynthesis using XFELs.
  Simon PS, Makita H, Bogacz I, Fuller F, Bhowmick A, Hussein R, Ibrahim M, Zhang M, Chatterjee R, Cheah MH, Chernev P, Doyle MD, Brewster AS, Alonso-Mori R, Sauter NK, Bergmann U, Dobbek H, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J.
  FEBS Lett 597, 30-37. (1 Jan 2023): [PMID:36310373] [Free PMC reprint: PMC9839502]

• Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b-NrdI complex monitored by serial femtosecond crystallography.
  John J, Aurelius O, Srinivas V, Saura P, Kim IS, Bhowmick A, Simon PS, Dasgupta M, Pham C, Gul S, Sutherlin KD, Aller P, Butryn A, Orville AM, Cheah MH, Owada S, Tono K, Fuller FD, Batyuk A, Brewster AS, Sauter NK, Yachandra VK, Yano J, Kaila VRI, Kern J, Lebrette H, Högbom M.
  Elife 11, e79226. (09 Sep 2022): [PMID:36083619] [Free PMC reprint: PMC9462851]
• De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals.
  Tetreau G, Sawaya MR, De Zitter E, Andreeva EA, Banneville AS, Schibrowsky NA, Coquelle N, Brewster AS, Grünbein ML, Kovacs GN, Hunter MS, Kloos M, Sierra RG, Schiro G, Qiao P, Stricker M, Bideshi D, Young ID, Zala N, Engilberge S, Gorel A, Signor L, Teulon JM, Hilpert M, Foucar L, Bielecki J, Bean R, de Wijn R, Sato T, Kirkwood H, Letrun R, Batyuk A, Snigireva I, Fenel D, Schubert R, Canfield EJ, Alba MM, Laporte F, Després L, Bacia M, Roux A, Chapelle C, Riobé F, Maury O, Ling WL, Boutet S, Mancuso A, Gutsche I, Girard E, Barends TRM, Pellequer JL, Park HW, Laganowsky AD, Rodriguez J, Burghammer M, Shoeman RL, Doak RB, Weik M, Sauter NK, Federici B, Cascio D, Schlichting I, Colletier JP.
  Nat Commun 13, 4376. (28 Jul 2022): [PMID:35902572] [Free PMC reprint: PMC9334358]
• XFEL serial crystallography reveals the room temperature structure of methyl-coenzyme M reductase.
  Ohmer CJ, Dasgupta M, Patwardhan A, Bogacz I, Kaminsky C, Doyle MD, Chen PY, Keable SM, Makita H, Simon PS, Massad R, Fransson T, Chatterjee R, Bhowmick A, Paley DW, Moriarty NW, Brewster AS, Gee LB, Alonso-Mori R, Moss F, Fuller FD, Batyuk A, Sauter NK, Bergmann U, Drennan CL, Yachandra VK, Yano J, Kern JF, Ragsdale SW.
  J Inorg Biochem 230, 111768. (17 Feb 2022): [PMID:35202981] [Free PMC reprint: PMC8930625]
• Chemical crystallography by serial femtosecond X-ray diffraction.
  Schriber EA, Paley DW, Bolotovsky R, Rosenberg DJ, Sierra RG, Aquila A, Mendez D, Poitevin F, Blaschke JP, Bhowmick A, Kelly RP, Hunter M, Hayes B, Popple DC, Yeung M, Pareja-Rivera C, Lisova S, Tono K, Sugahara M, Owada S, Kuykendall T, Yao K, Schuck PJ, Solis-Ibarra D, Sauter NK, Brewster AS, Hohman JN.
  Nature 601, 360-365. (1 Jan 2022): [PMID:35046599] [Free PMC reprint: PMC8770144] (LBNL Press release) (SLAC Press release) (SharedIT https://rdcu.be/cFi65) (phys.org story)
• Global data management and provenance
  Brewster AS, Blaschke J, Maia FRNC, Kern J (Jan 2022) DOE ASCR Workshop on the Management and Storage of Scientific Data. Position paper.

• The challenges of scientific software sustainability.
  Brewster AS, Liebschner D, Poon BK, Sauter NK, and Adams PD (Dec. 2021). DOE ASCR Workshop on the Science of Scientific-Software Development and Use. Position paper.
• Structural dynamics in the water and proton channels of photosystem II during the S₂ to S₃ transition.
  Hussein R, Ibrahim M, Bhowmick A, Simon PS, Chatterjee R, Lassalle L, Doyle M, Bogacz I, Kim IS, Cheah MH, Gul S, de Lichtenberg C, Chernev P, Pham CC, Young ID, Carbajo S, Fuller FD, Alonso-Mori R, Batyuk A, Sutherlin KD, Brewster AS, Bolotovsky R, Mendez D, Holton JM, Moriarty NW, Adams PD, Bergmann U, Sauter NK, Dobbek H, Messinger J, Zouni A, Kern J, Yachandra VK, Yano J.
  Nat Commun 12, 6531. (11 11 2021): [PMID:34764256] [Free PMC reprint: PMC8585918] (LBNL Press release) (SLAC Press release)
• Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I.
  Keable SM, Kölsch A, Simon PS, Dasgupta M, Chatterjee R, Subramanian SK, Hussein R, Ibrahim M, Kim IS, Bogacz I, Makita H, Pham CC, Fuller FD, Gul S, Paley D, Lassalle L, Sutherlin KD, Bhowmick A, Moriarty NW, Young ID, Blaschke JP, de Lichtenberg C, Chernev P, Cheah MH, Park S, Park G, Kim J, Lee SJ, Park J, Tono K, Owada S, Hunter MS, Batyuk A, Oggenfuss R, Sander M, Zerdane S, Ozerov D, Nass K, Lemke H, Mankowsky R, Brewster AS, Messinger J, Sauter NK, Yachandra VK, Yano J, Zouni A, Kern J.
  Sci Rep 11, 21787. (08 Nov 2021): [PMID:34750381] [Free PMC reprint: PMC8575901] (SharedIT https://rdcu.be/cA0uM)
• X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis.
  Rabe P, Kamps JJAG, Sutherlin KD, Linyard JDS, Aller P, Pham CC, Makita H, Clifton I, McDonough MA, Leissing TM, Shutin D, Lang PA, Butryn A, Brem J, Gul S, Fuller FD, Kim IS, Cheah MH, Fransson T, Bhowmick A, Young ID, O'Riordan L, Brewster AS, Pettinati I, Doyle M, Joti Y, Owada S, Tono K, Batyuk A, Hunter MS, Alonso-Mori R, Bergmann U, Owen RL, Sauter NK, Claridge TDW, Robinson CV, Yachandra VK, Yano J, Kern JF, Orville AM, Schofield CJ.
  Sci Adv 7, eabh0250. (1 Aug 2021): [PMID:34417180] [Free PMC reprint: PMC8378823] (LBNL Press release)
• An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography.
  Butryn A, Simon PS, Aller P, Hinchliffe P, Massad RN, Leen G, Tooke CL, Bogacz I, Kim IS, Bhowmick A, Brewster AS, Devenish NE, Brem J, Kamps JJAG, Lang PA, Rabe P, Axford D, Beale JH, Davy B, Ebrahim A, Orlans J, Storm SLS, Zhou T, Owada S, Tanaka R, Tono K, Evans G, Owen RL, Houle FA, Sauter NK, Schofield CJ, Spencer J, Yachandra VK, Yano J, Kern JF, Orville AM.
  Nat Commun 12, 4461. (22 07 2021): [PMID:34294694] [Free PMC reprint: PMC8298390] (LBNL Press release)
• Real-Time XFEL Data Analysis at SLAC and NERSC: a Trial Run of Nascent Exascale Experimental Data Analysis.
  Blaschke JP, Brewster AS, Paley DW, Mendez D, Bhowmick A, Sauter NK, Kröger W, Shankar M, Enders B, Bard D.
  ArXiv (22 Jun 2021): [PMID:34189183] [Free PMC reprint: PMC8240685]
• Reply to Wang et al.: Clear evidence of binding of Ox to the oxygen-evolving complex of photosystem II is best observed in the omit map.
  Ibrahim M, Moriarty NW, Kern J, Holton JM, Brewster AS, Bhowmick A, Bergmann U, Zouni A, Messinger J, Yachandra VK, Yano J, Dobbek H, Sauter NK, Adams PD.
  Proc Natl Acad Sci U S A 118, e2102342118. (15 06 2021): [PMID:34117122] [Free PMC reprint: PMC8214684]
• Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation.
  Peck A, Yao Q, Brewster AS, Zwart PH, Heumann JM, Sauter NK, Jensen GJ.
  Acta Crystallogr D Struct Biol 77, 572-586. (01 May 2021): [PMID:33950014] [Free PMC reprint: PMC8098477]

• Beyond integration: modeling every pixel to obtain better structure factors from stills.
  Mendez D, Bolotovsky R, Bhowmick A, Brewster AS, Kern J, Yano J, Holton JM, Sauter NK.
  IUCrJ 7, 1151-1167. (01 Nov 2020): [PMID:33209326] [Free PMC reprint: PMC7642780] (LBNL Press release) (Journal Commentary)
• High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States.
  Srinivas V, Banerjee R, Lebrette H, Jones JC, Aurelius O, Kim IS, Pham CC, Gul S, Sutherlin KD, Bhowmick A, John J, Bozkurt E, Fransson T, Aller P, Butryn A, Bogacz I, Simon P, Keable S, Britz A, Tono K, Kim KS, Park SY, Lee SJ, Park J, Alonso-Mori R, Fuller FD, Batyuk A, Brewster AS, Bergmann U, Sauter NK, Orville AM, Yachandra VK, Yano J, Lipscomb JD, Kern J, Högbom M.
  J Am Chem Soc 142, 14249-14266. (19 Aug 2020): [PMID:32683863] [Free PMC reprint: PMC7457426] (LBNL Press release)
• Gold Standard for macromolecular crystallography diffraction data.
  Bernstein HJ, Förster A, Bhowmick A, Brewster AS, Brockhauser S, Gelisio L, Hall DR, Leonarski F, Mariani V, Santoni G, Vonrheink C, Winter G
  IUCrJ 7, 784-792. (10 July 2020): [PMID:32939270] [Free PMC reprint: PMC7467160]
• Untangling the sequence of events during the S₂ → S₃ transition in photosystem II and implications for the water oxidation mechanism.
  Ibrahim M, Fransson T, Chatterjee R, Cheah MH, Hussein R, Lassalle L, Sutherlin KD, Young ID, Fuller FD, Gul S, Kim IS, Simon PS, de Lichtenberg C, Chernev P, Bogacz I, Pham CC, Orville AM, Saichek N, Northen T, Batyuk A, Carbajo S, Alonso-Mori R, Tono K, Owada S, Bhowmick A, Bolotovsky R, Mendez D, Moriarty NW, Holton JM, Dobbek H, Brewster AS, Adams PD, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J.
  Proc. Natl. Acad. Sci. U.S.A. 117, 12624-12635. (09 Jun 2020): [PMID:32434915] [Free PMC reprint: PMC7293653] (LBNL Press release) (Daily Californian)
• Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases.
  Miller KR, Paretsky JD, Follmer AH, Heinisch T, Mittra K, Gul S, Kim IS, Fuller FD, Batyuk A, Sutherlin KD, Brewster AS, Bhowmick A, Sauter NK, Kern J, Yano J, Green MT, Ward TR, Borovik AS.
  Inorg Chem 59, 6000-6009. (04 May 2020): [PMID:32309932] [PMC reprint: PMC7219546]
• Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals.
  Wolff AM, Young ID, Sierra RG, Brewster AS, Martynowycz MW, Nango E, Sugahara M, Nakane T, Ito K, Aquila A, Bhowmick A, Biel JT, Carbajo S, Cohen AE, Cortez S, Gonzalez A, Hino T, Im D, Koralek JD, Kubo M, Lazarou TS, Nomura T, Owada S, Samelson AJ, Tanaka T, Tanaka R, Thompson EM, van den Bedem H, Woldeyes RA, Yumoto F, Zhao W, Tono K, Boutet S, Iwata S, Gonen T, Sauter NK, Fraser JS, Thompson MC.
  IUCrJ 7, 306-323. (01 Mar 2020): [PMID:32148858] [PMC reprint: PMC7055375]
• Serial femtosecond crystallography on in vivo-grown crystals drives elucidation of mosquitocidal Cyt1Aa bioactivation cascade.
  Tetreau G, Banneville AS, Andreeva EA, Brewster AS, Hunter MS, Sierra RG, Teulon JM, Young ID, Burke N, Grünewald TA, Beaudouin J, Snigireva I, Fernandez-Luna MT, Burt A, Park HW, Signor L, Bafna JA, Sadir R, Fenel D, Boeri-Erba E, Bacia M, Zala N, Laporte F, Després L, Weik M, Boutet S, Rosenthal M, Coquelle N, Burghammer M, Cascio D, Sawaya MR, Winterhalter M, Gratton E, Gutsche I, Federici B, Pellequer JL, Sauter NK, Colletier JP.
  Nat Commun 11, 1153. (02 03 2020): [PMID:32123169] [PMC reprint: PMC7052140] (LBNL Press release)
• Photoreversible interconversion of a phytochrome photosensory module in the crystalline state.
  Burgie ES, Clinger JA, Miller MD, Brewster AS, Aller P, Butryn A, Fuller FD, Gul S, Young ID, Pham CC, Kim IS, Bhowmick A, O'Riordan LJ, Sutherlin KD, Heinemann JV, Batyuk A, Alonso-Mori R, Hunter MS, Koglin JE, Yano J, Yachandra VK, Sauter NK, Cohen AE, Kern J, Orville AM, Phillips GN, Vierstra RD.
  Proc. Natl. Acad. Sci. U.S.A. 117, 300-307. (07 01 2020): [PMID:31852825] [PMC reprint: PMC6955287]

• Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.
  Dasgupta M, Budday D, de Oliveira SHP, Madzelan P, Marchany-Rivera D, Seravalli J, Hayes B, Sierra RG, Boutet S, Hunter MS, Alonso-Mori R, Batyuk A, Wierman J, Lyubimov A, Brewster AS, Sauter NK, Applegate GA, Tiwari VK, Berkowitz DB, Thompson MC, Cohen AE, Fraser JS, Wall ME, van den Bedem H, Wilson MA.
  Proc. Natl. Acad. Sci. U.S.A. 116, 25634-25640. (17 12 2019): [PMID:31801874] [PMC reprint: PMC6926069]
• SAD phasing of XFEL data depends critically on the error model.
  Brewster AS, Bhowmick A, Bolotovsky R, Mendez D, Zwart PH, Sauter NK.
  Acta Crystallogr D Struct Biol 75, 959-968. (01 Nov 2019): [PMID:31692470] [PMC reprint: PMC6834081]
• The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity.
  Barnes CO, Wu Y, Song J, Lin G, Baxter EL, Brewster AS, Nagarajan V, Holmes A, Soltis SM, Sauter NK, Ahn J, Cohen AE, Calero G.
  Proc. Natl. Acad. Sci. U.S.A. 116, 9333-9339. (07 May 2019): [PMID:31019074]
• Brewster AS, Young ID, Lyubimov A, Bhowmick A, Sauter NK (2019): Processing serial crystallographic data from XFELs or synchrotrons using the cctbx.xfel GUI. Computational Crystallography Newsletter 10, 22-39. (Reprint)

• Structures of the intermediates of Kok's photosynthetic water oxidation clock.
  Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK.
  Nature 563, 421-425. (1 11 2018): [PMID:30405241] [Free PMC reprint: PMC6485242] (LBNL Press release) (SLAC Press release) (SharedIt http://rdcu.be/bbwH7)
• Improving signal strength in serial crystallography with DIALS geometry refinement.
  Brewster AS, Waterman DG, Parkhurst JM, Gildea RJ, Young ID, O'Riordan LJ, Yano J, Winter G, Evans G, Sauter NK.
  Acta Crystallogr D Struct Biol 74, 877-894. (01 Sep 2018): [PMID:30198898] [PMC reprint: PMC6130462]
• A convolutional neural network-based screening tool for X-ray serial crystallography.
  Ke TW, Brewster AS, Yu SX, Ushizima D, Yang C, Sauter NK.
  J Synchrotron Radiat 25, 655-670. (01 May 2018): [PMID:29714177] [PMC reprint: PMC5929353]
• DIALS: implementation and evaluation of a new integration package.
  Winter G, Waterman DG, Parkhurst JM, Brewster AS, Gildea RJ, Gerstel M, Fuentes-Montero L, Vollmar M, Michels-Clark T, Young ID, Sauter NK, Evans G.
  Acta Crystallogr D Struct Biol 74, 85-97. (01 Feb 2018): [PMID:29533234] [Free PMC reprint: PMC5947772]
• Towards in cellulo virus crystallography.
  Duyvesteyn HME, Ginn HM, Pietilä MK, Wagner A, Hattne J, Grimes JM, Hirvonen E, Evans G, Parsy ML, Sauter NK, Brewster AS, Huiskonen JT, Stuart DI, Sutton G, Bamford DH.
  Sci Rep 8, 3771. (28 Feb 2018): [PMID:29491457] [PMC reprint: PMC5830620]

• XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction.
  Thomaston JL, Woldeyes RA, Nakane T, Yamashita A, Tanaka T, Koiwai K, Brewster AS, Barad BA, Chen Y, Lemmin T, Uervirojnangkoorn M, Arima T, Kobayashi J, Masuda T, Suzuki M, Sugahara M, Sauter NK, Tanaka R, Nureki O, Tono K, Joti Y, Nango E, Iwata S, Yumoto F, Fraser JS, DeGrado WF.
  Proc. Natl. Acad. Sci. U.S.A. 114, 13357-13362. (19 Dec 2017): [PMID:28835537] [PMC reprint: PMC5754760]
• High-speed fixed-target serial virus crystallography.
  Roedig P, Ginn HM, Pakendorf T, Sutton G, Harlos K, Walter TS, Meyer J, Fischer P, Duman R, Vartiainen I, Reime B, Warmer M, Brewster AS, Young ID, Michels-Clark T, Sauter NK, Kotecha A, Kelly J, Rowlands DJ, Sikorsky M, Nelson S, Damiani DS, Alonso-Mori R, Ren J, Fry EE, David C, Stuart DI, Wagner A, Meents A.
  Nat. Methods 14, 805-810. (1 Aug 2017): [PMID:28628129] [PMC reprint: PMC5588887] (SharedIt http://rdcu.be/tyvU)
• Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser.
  Popp D, Loh ND, Zorgati H, Ghoshdastider U, Liow LT, Ivanova MI, Larsson M, DePonte DP, Bean R, Beyerlein KR, Gati C, Oberthuer D, Arnlund D, Brändén G, Berntsen P, Cascio D, Chavas LMG, Chen JPJ, Ding K, Fleckenstein H, Gumprecht L, Harimoorthy R, Mossou E, Sawaya MR, Brewster AS, Hattne J, Sauter NK, Seibert M, Seuring C, Stellato F, Tilp T, Eisenberg DS, Messerschmidt M, Williams GJ, Koglin JE, Makowski L, Millane RP, Forsyth T, Boutet S, White TA, Barty A, Chapman H, Chen SL, Liang M, Neutze R, Robinson RC.
  Cytoskeleton (Hoboken) 74(12), 472-481. (02 Jun 2017): [PMID:28574190]
• Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers.
  Fuller FD, Gul S, Chatterjee R, Burgie ES, Young ID, Lebrette H, Srinivas V, Brewster AS, Michels-Clark T, Clinger JA, Andi B, Ibrahim M, Pastor E, de Lichtenberg C, Hussein R, Pollock CJ, Zhang M, Stan CA, Kroll T, Fransson T, Weninger C, Kubin M, Aller P, Lassalle L, Bräuer P, Miller MD, Amin M, Koroidov S, Roessler CG, Allaire M, Sierra RG, Docker PT, Glownia JM, Nelson S, Koglin JE, Zhu D, Chollet M, Song S, Lemke H, Liang M, Sokaras D, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Boal AK, Bollinger JM, Krebs C, Högbom M, Phillips GN, Vierstra RD, Sauter NK, Orville AM, Kern J, Yachandra VK, Yano J.
  Nat. Methods 14, 443-449. (1 Apr 2017): [PMID:28250468] [PMC reprint: PMC5376230] (SLAC Press release) (SharedIt http://rdcu.be/pDdy)
• Poon BK, Brewster AS, Sauter NK (2017): Deploying cctbx.xfel in Cloud Computing and High Performance Computing Environments. Computational Crystallography Newsletter 8, 10-19. (Reprint)

• Structure of photosystem II and substrate binding at room temperature.
  Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller FD, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Vo Pham L, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng TC, Pastor E, Weninger C, Fransson T, Lassalle L, Bräuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Lane TJ, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty NW, Liebschner D, Afonine PV, Waterman DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams PD, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, Yano J.
  Nature 540, 453-457. (15 Dec 2016): [PMID:27871088] [PMC reprint: PMC5201176] (SLAC Press release) (LBNL Press release) (LBNL Photo) (SharedIt http://rdcu.be/mPXr)
• Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Zhou Q, Zhao M, Brewster AS, Michels-Clark T, Holton JM, Sauter NK, Weis WI, Brunger AT (12 Oct 2016): Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex. Elife 5, [PMID:27731796] [PMC reprint: PMC5094853]
• Colletier JP, Sawaya MR, Gingery M, Rodriguez JA, Cascio D, Brewster AS, Michels-Clark T, Hice RH, Coquelle N, Boutet S, Williams GJ, Messerschmidt M, DePonte DP, Sierra RG, Laksmono H, Koglin JE, Hunter MS, Park HW, Uervirojnangkoorn M, Bideshi DK, Brunger AT, Federici BA, Sauter NK, Eisenberg DS (28 Sep 2016): De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure. Nature 539, 43-47. [PMID:27680699] [Free PMC reprint: PMC5161637] (SLAC Press release) (LBNL Press release) (SharedIt http://rdcu.be/msVB)
• Brewster AS, Waterman DG, Parkhurst JM, Gildea RJ, Michels-Clark TM, Young ID, Bernstein HJ, Winter G, Evans G, Sauter NK (2016): Processing XFEL data with cctbx.xfel and DIALS. Computational Crystallography Newsletter 7, 32-53. (Reprint)
• Towards characterization of photo-excited electron transfer and catalysis in natural and artificial systems using XFELs.
  Alonso-Mori R, Asa K, Bergmann U, Brewster AS, Chatterjee R, Cooper JK, Frei HM, Fuller FD, Goggins E, Gul S, Fukuzawa H, Iablonskyi D, Ibrahim M, Katayama T, Kroll T, Kumagai Y, McClure BA, Messinger J, Motomura K, Nagaya K, Nishiyama T, Saracini C, Sato Y, Sauter NK, Sokaras D, Takanashi T, Togashi T, Ueda K, Weare WW, Weng TC, Yabashi M, Yachandra VK, Young ID, Zouni A, Kern JF, Yano J.
  Faraday Discuss. 194, 621-638. (16 Dec 2016): [PMID:27711803] [PMC reprint: PMC5177497]
• Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Brewster AB, Murray TD, Sauter NK, Berger JM, Weis WI, Brunger AT (Jun 2016): IOTA: integration optimization, triage and analysis tool for the processing of XFEL diffraction images J Appl Cryst 49, 1057-1064.
• Sauter NK, Echols N, Adams PD, Zwart PH, Kern J, Brewster AS, Koroidov S, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Yano J, Yachandra VK (19 May 2016): No observable conformational changes in PSII. Nature 533, E1-2. [PMID:27193689]
• Waterman DG, Winter G, Gildea RJ, Parkhurst JM, Brewster AS, Sauter NK, Evans G (1 Apr 2016): Diffraction-geometry refinement in the DIALS framework. Acta Crystallogr D Struct Biol 72, 558-75. [PMID:27050135] [PMC reprint: PMC4822564]
• Van Benschoten AH, Liu L, Gonzalez A, Brewster AS, Sauter NK, Fraser JS, Wall ME (28 Mar 2016): Measuring and modeling diffuse scattering in protein X-ray crystallography. Proc. Natl. Acad. Sci. U.S.A. 113 (15):4069-4074. [PMID:27035972] [PMC reprint: PMC4839442]
• Roessler CG, Agarwal R, Allaire M, Alonso-Mori R, Andi B, Bachega JF, Bommer M, Brewster AS, Browne MC, Chatterjee R, Cho E, Cohen AE, Cowan M, Datwani S, Davidson VL, Defever J, Eaton B, Ellson R, Feng Y, Ghislain LP, Glownia JM, Han G, Hattne J, Hellmich J, Héroux A, Ibrahim M, Kern J, Kuczewski A, Lemke HT, Liu P, Majlof L, McClintock WM, Myers S, Nelsen S, Olechno J, Orville AM, Sauter NK, Soares AS, Soltis SM, Song H, Stearns RG, Tran R, Tsai Y, Uervirojnangkoorn M, Wilmot CM, Yachandra V, Yano J, Yukl ET, Zhu D, Zouni A (5 Apr 2016): Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography. Structure 24, 631-40. [PMID:26996959]
• Barnes CO, Kovaleva EG, Fu X, Stevenson HP, Brewster AS, DePonte DP, Baxter EL, Cohen AE, Calero G (2 Mar 2016): Assessment of microcrystal quality by transmission electron microscopy for efficient serial femtosecond crystallography. Arch Biochem Biophys. 602, 61-68.
[PMID:26944553]

2015

• Sierra RG, Gati C, Laksmono H, Dao EH, Gul S, Fuller F, Kern J, Chatterjee R, Ibrahim M, Brewster AS, Young ID, Michels-Clark T, Aquila A, Liang M, Hunter MS, Koglin JE, Boutet S, Junco EA, Hayes B, Bogan MJ, Hampton CY, Puglisi EV, Sauter NK, Stan CA, Zouni A, Yano J, Yachandra VK, Soltis SM, Puglisi JD, DeMirci H (30 Nov 2015): Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II. Nat. Methods [PMID:26619013]
• Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS (30 Sep 2015): Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. Elife 4, e07574. [PMID:26422513] [Free PMC reprint: PMC4721965]
• Rodriguez JA, Ivanova MI, Sawaya MR, Cascio D, Reyes FE, Shi D, Sangwan S, Guenther EL, Johnson LM, Zhang M, Jiang L, Arbing MA, Nannenga BL, Hattne J, Whitelegge J, Brewster AS, Messerschmidt M, Boutet S, Sauter NK, Gonen T, Eisenberg DS (9 Sep 2015): Structure of the toxic core of α-synuclein from invisible crystals. Nature 525, 486-490. [PMID:26352473] [Free PMC reprint: PMC4791177]
• Zhou Q, Lai Y, Bacaj T, Zhao M, Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Brewster AS, Sauter NK, Cohen AE, Soltis SM, Alonso-Mori R, Chollet M, Lemke HT, Pfuetzner RA, Choi UB, Weis WI, Diao J, Südhof TC, Brunger AT (3 Sep 2015): Architecture of the synaptotagmin-SNARE machinery for neuronal exocytosis. Nature 525, 62-7. [PMID:26280336] [Free PMC reprint: PMC4607316] (Press release)
• Ginn HM, Brewster AS, Hattne J, Evans G, Wagner A, Grimes JM, Sauter NK, Sutton G, Stuart DI (May 2015): A revised partiality model and post-refinement algorithm for X-ray free-electron laser data Acta Crystallogr. D Biol. Crystallogr. 71, (6):1400-10. [PMID:26057680] [PMC reprint: PMC4461207]
• Coquelle N, Brewster AS, Kapp U, Shilova A, Weinhausen B, Burghammer M, Colletier JP (May 2015): Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams Acta Crystallogr. D Biol. Crystallogr. 71, (5):1184-96. [PMID:25945583] [PMC reprint: PMC4427202]
• Lyubimov AY, Murray TD, Koehl A, Araci IE, Uervirojnangkoorn M, Zeldin OB, Cohen AE, Soltis SM, Baxter EL, Brewster AS, Sauter NK, Brunger AT, Berger JM (1 Apr 2015): Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array. Acta Crystallogr. D Biol. Crystallogr. 71, 928-40. [PMID:25849403] [PMC reprint: PMC4388268]
• Uervirojnangkoorn M, Zeldin OB, Lyubimov AY, Hattne J, Brewster AS, Sauter NK, Brunger AT, Weis WI (2015): Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals. Elife 4, . [PMID:25781634] [PMC reprint: PMC4397907]
• Könnecke M, Akeroyd FA, Bernstein HJ, Brewster AS, Campbell SI, Clausen B, Cottrell S, Hoffmann JU, Jemian PR, Männicke D, Osborn R, Peterson PF, Richter T, Suzuki J, Watts B, Wintersberger E, Wuttke J (2015): The NeXus data format. J Appl Cryst 48, 301-305. [PMID:26089752] [PMC reprint: PMC4453170]
• Ginn HM, Messerschmidt M, Ji X, Zhang H, Axford D, Gildea RJ, Winter G, Brewster AS, Hattne J, Wagner A, Grimes JM, Evans G, Sauter NK, Sutton G, Stuart DI (2015): Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data. Nat Commun 6, 6435. [PMID:25751308] [PMC reprint: PMC4403592]
• Brewster AS, Sawaya MR, Rodriguez J, Hattne J, Echols N, McFarlane HT, Cascio D, Adams PD, Eisenberg DS, Sauter NK (1 Feb 2015): Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns. Acta Crystallogr. D Biol. Crystallogr. 71, 357-66. [PMID:25664747] [PMC reprint: PMC4321489]
• Zeldin OB, Brewster AS, Hattne J, Uervirojnangkoorn M, Lyubimov AY, Zhou Q, Zhao M, Weis WI, Sauter NK, Brunger AT (1 Feb 2015): Data Exploration Toolkit for serial diffraction experiments. Acta Crystallogr. D Biol. Crystallogr. 71, 352-6. [PMID:25664746] [PMC reprint: PMC4321488]

• Sauter NK, Hattne J, Brewster AS, Echols N, Zwart PH, Adams PD (1 Dec 2014): Improved crystal orientation and physical properties from single-shot XFEL stills. Acta Crystallogr. D Biol. Crystallogr. 70, 3299-309. [PMID:25478847] [PMC reprint: PMC4257623] (Reprint)
• Cohen AE, Soltis SM, González A, Aguila L, Alonso-Mori R, Barnes CO, Baxter EL, Brehmer W, Brewster AS, Brunger AT, Calero G, Chang JF, Chollet M, Ehrensberger P, Eriksson TL, Feng Y, Hattne J, Hedman B, Hollenbeck M, Holton JM, Keable S, Kobilka BK, Kovaleva EG, Kruse AC, Lemke HT, Lin G, Lyubimov AY, Manglik A, Mathews II, McPhillips SE, Nelson S, Peters JW, Sauter NK, Smith CA, Song J, Stevenson HP, Tsai Y, Uervirojnangkoorn M, Vinetsky V, Wakatsuki S, Weis WI, Zadvornyy OA, Zeldin OB, Zhu D, Hodgson KO (2 Dec 2014): Goniometer-based femtosecond crystallography with X-ray free electron lasers. Proc. Natl. Acad. Sci. U.S.A. 111, 17122-7. [PMID:25362050] [PMC reprint: PMC4260607]
• Sawaya MR, Cascio D, Gingery M, Rodriguez J, Goldschmidt L, Colletier JP, Messerschmidt MM, Boutet S, Koglin JE, Williams GJ, Brewster AS, Nass K, Hattne J, Botha S, Doak RB, Shoeman RL, DePonte DP, Park HW, Federici BA, Sauter NK, Schlichting I, Eisenberg DS (2 Sep 2014): Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam. Proc. Natl. Acad. Sci. U.S.A. 111, 12769-74. [PMID:25136092] [PMC reprint: PMC4156696] (Reprint)
• Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glöckner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE, Gallo E, Uhlig J, Sokaras D, Weng TC, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK (2014): Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nat Commun 5, 4371. [PMID:25006873] [PMC reprint: PMC4151126]
• Parkhurst JM, Brewster AS, Fuentes-Montero L, Waterman DG, Hattne J, Ashton AW, Echols N, Evans G, Sauter NK, Winter G (1 Aug 2014): dxtbx: the diffraction experiment toolbox. J Appl Crystallogr 47, 1459-1465. [PMID:25242914] [PMC reprint: PMC4119952] (Reprint)
• Hattne J, Echols N, Tran R, Kern J, Gildea RJ, Brewster AS, Alonso-Mori R, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Lampe A, Han G, Gul S, Difiore D, Milathianaki D, Fry AR, Miahnahri A, White WE, Schafer DW, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Glatzel P, Zwart PH, Grosse-Kunstleve RW, Bogan MJ, Messerschmidt M, Williams GJ, Boutet S, Messinger J, Zouni A, Yano J, Bergmann U, Yachandra VK, Adams PD, Sauter NK: Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nature Methods 2014, 11:545-8 [PMID:24633409]
• Brewster AS, Hattne J, Parkhurst JM, Waterman DG, Bernstein HJ, Winter G, Sauter NK (2014): XFEL Detectors and ImageCIF. Computational Crystallography Newsletter 5, 19-24. (Reprint)

• Waterman DG, Winter G, Parkhurst JM, Fuentes-Montero L, Hattne J, Brewster A, Sauter NK, Evans G (2013): The DIALS framework for integration software. CCP4 Newsletter on Protein Crystallography 49, 16-19. (Reprint)

• Slaymaker I, Fu Y, Toso DB, Ranatunga N, Brewster A, Forsburg SL, Zhou ZH, Chen XS: Mini-chromosome maintenance complexes form a filament to remodel DNA structure and topology. Nucleic Acids Research 2013, 41(5):3446-56 [PMID:23361460]

2012

• Zhou B, Arnett DR, Yu X, Brewster A, Sowd GA, Xie CL, Vila S, Gai D, Fanning E, Chen XS: Structural Basis for the Interaction of a Hexameric Replicative Helicase with the Regulatory Subunit of Human DNA Polymerase α-Primase. J Biol Chem 2012, 287(32):26854-66 [PMID:22700977]

2010

• Brewster AS, Slaymaker IM, Afif SA, Chen XS: Mutational Analysis of an Archaeal Minichromosome Maintenance Protein Exterior Hairpin Reveals Critical Residues for Helicase Activity and DNA Binding. BMC Mol Biol 2010, 1162 [PMID:20716382]

2009

• Brewster AS, Chen XS: Insights Into MCM Functional Mechanism: Lessons Learned From the Archaeal MCM Complex. Crit Rev Biochem Mol Biol 2010, 45(3):243-56 [PMID:20441442]

2008

• Brewster AS, Wang G, Yu X, Greenleaf WB, Carazo JM, Tjajadi M, Klein MG, Chen XS: Crystal structure of a near-full-length archaeal MCM: functional insights for an AAA+ hexameric helicase. Proc Natl Acad Sci U S A 2008,105(51):20191-6 [PMID:19073923]