The solvent component of macromolecular crystals
Christian X. Weichenberger,Pavel V. Afonine,Katherine A. Kantardjieff,Bernhard Rupp,Bernhard Rupp +4 more
TLDR
On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal.Abstract:
The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initial phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.read more
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“Bioinformatics” 특집을 내면서
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Polder maps: improving OMIT maps by excluding bulk solvent.
Dorothee Liebschner,Pavel V. Afonine,Nigel W. Moriarty,Billy K. Poon,Oleg V. Sobolev,Thomas C. Terwilliger,Paul D. Adams,Paul D. Adams +7 more
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Structure of photosystem II and substrate binding at room temperature
Iris D. Young,Mohamed Ibrahim,Ruchira Chatterjee,Sheraz Gul,Franklin D. Fuller,Sergey Koroidov,Aaron S. Brewster,Rosalie Tran,Roberto Alonso-Mori,Thomas Kroll,Tara Michels-Clark,Hartawan Laksmono,Raymond G. Sierra,Claudiu A. Stan,Rana Hussein,Miao Zhang,Lacey Douthit,Markus Kubin,Casper de Lichtenberg,Long Vo Pham,Håkan Nilsson,Mun Hon Cheah,Dmitriy Shevela,Claudio Saracini,Mackenzie A. Bean,Ina Seuffert,Dimosthenis Sokaras,Tsu-Chien Weng,Ernest Pastor,Clemens Weninger,Thomas Fransson,Louise Lassalle,Philipp Bräuer,Pierre Aller,P. T. Docker,Babak Andi,Allen M. Orville,James M. Glownia,Silke Nelson,Marcin Sikorski,Diling Zhu,Mark S. Hunter,Thomas J. Lane,Andrew Aquila,Jason E. Koglin,Joseph Robinson,Mengning Liang,Sébastien Boutet,Artem Y. Lyubimov,Artem Y. Lyubimov,Monarin Uervirojnangkoorn,Monarin Uervirojnangkoorn,Nigel W. Moriarty,Dorothee Liebschner,Pavel V. Afonine,David G. Waterman,Gwyndaf Evans,Philippe Wernet,Holger Dobbek,William I. Weis,Axel T. Brunger,Petrus H. Zwart,Paul D. Adams,Paul D. Adams,Athina Zouni,Johannes Messinger,Johannes Messinger,Uwe Bergmann,Nicholas K. Sauter,Jan Kern,Jan Kern,Vittal K. Yachandra,Junko Yano +72 more
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Mg2+ ions: do they bind to nucleobase nitrogens?
TL;DR: A potential Zn2+ ribosomal binding site involving two purine N7 atoms is described and a set of guidelines are provided to help in the assignment of Mg2+ in crystallographic, cryo-EM, NMR and model building practices.
References
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