In situ ligand restraints from quantum-mechanical methods.
Autorzy:
Liebschner D; Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. MoriartyNW; Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Poon BK; Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Adams PD; Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Liu Y; International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China. Biczysko M; International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China. MoriartyNW; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA.
Room temperature XFEL crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem I.
Autorzy:
Keable SM; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Kölsch A; Institut für Biologie, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany. Simon PS; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Dasgupta M; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Chatterjee R; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Subramanian SK; Institut für Biologie, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany. Hussein R; Institut für Biologie, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany. Ibrahim M; Institut für Biologie, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany. Kim IS; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Bogacz I; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Makita H; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Pham CC; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Fuller FD; LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA. Gul S; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Paley D; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Lassalle L; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Sutherlin KD; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Bhowmick A; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. MoriartyNW; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Young ID; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, 94158, USA. Blaschke JP; National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. de Lichtenberg C; Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, 75237, Uppsala, Sweden.; Department of Chemistry, Umeå University, Linnaeus väg 6 (KBC huset), 90187, Umeå, Sweden. Chernev P; Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, 75237, Uppsala, Sweden. Cheah MH; Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, 75237, Uppsala, Sweden. Park S; Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Korea. Park G; Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Korea. Kim J; Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Korea. Lee SJ; Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Korea. Park J; Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Korea. Tono K; Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan. Owada S; Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan.; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan. Hunter MS; LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA. Batyuk A; LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA. Oggenfuss R; Paul Scherrer Institut, 5232, Villigen, Switzerland. Sander M; Paul Scherrer Institut, 5232, Villigen, Switzerland. Zerdane S; Paul Scherrer Institut, 5232, Villigen, Switzerland. Ozerov D; Paul Scherrer Institut, 5232, Villigen, Switzerland. Nass K; Paul Scherrer Institut, 5232, Villigen, Switzerland. Lemke H; Paul Scherrer Institut, 5232, Villigen, Switzerland. Mankowsky R; Paul Scherrer Institut, 5232, Villigen, Switzerland. Brewster AS; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Messinger J; Department of Chemistry - Ångström, Molecular Biomimetics, Uppsala University, 75237, Uppsala, Sweden. Sauter NK; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Yachandra VK; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Yano J; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Zouni A; Institut für Biologie, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany. Kern J; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .
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Źródło:
Scientific reports [Sci Rep] 2021 Nov 08; Vol. 11 (1), pp. 21787. Date of Electronic Publication: 2021 Nov 08.
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models.
Autorzy:
Liebschner D; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA. Afonine PV; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA. MoriartyNW; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA. Poon BK; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA. Chen VB; Department of Biochemistry, Duke University, Durham, NC 27710, USA. Adams PD; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Real-space quantum-based refinement for cryo-EM: Q|R#3.
Autorzy:
Wang L; International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China. Kruse H; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic. Sobolev OV; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. MoriartyNW; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Waller MP; Pending AI Pty Ltd, iAccelerat, Innovation Campus, North Wollongong, NSW 2500, Australia. Afonine PV; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Biczysko M; International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China.
Arginine off-kilter: guanidinium is not as planar as restraints denote.
Autorzy:
MoriartyNW; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Liebschner D; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Tronrud DE; Department of Biochemistry and Biophysics and the Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA. Adams PD; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.
Autorzy:
MoriartyNW; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA. Janowski PA; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Swails JM; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Nguyen H; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Richardson JS; Department of Biochemistry, Duke University, Durham, NC 27710, USA. Case DA; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. Adams PD; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA.
Including crystallographic symmetry in quantum-based refinement: Q|R#2.
Autorzy:
Zheng M; International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China. Biczysko M; International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China. Xu Y; International Center for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China. MoriartyNW; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Kruse H; Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic. Urzhumtsev A; Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS-INSERM-UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France. Waller MP; Pending AI Pty Ltd, iAccelerate, Innovation Campus, Squires Way, North Wollongong, NSW 2500, Australia. Afonine PV; Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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