1. Bulk-solvent correction in large macromolecular structures
- Author
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B. Rees, Marat Yusupov, Lasse Jenner, Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Louis Pasteur - Strasbourg I, and Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Diffraction ,Macromolecular Substances ,MESH: Drug Interactions ,MESH: Solvents ,MESH: Thermus thermophilus ,010402 general chemistry ,MESH: Amlodipine ,01 natural sciences ,MESH: Mouth ,Crystal ,X-Ray Diffraction ,Structural Biology ,MESH: Tissue Plasminogen Activator ,MESH: Cerebrovascular Accident ,MESH: Treatment Outcome ,Variable (mathematics) ,MESH: Middle Aged ,MESH: Humans ,010405 organic chemistry ,Chemistry ,Thermus thermophilus ,MESH: Tongue ,Resolution (electron density) ,Isotropy ,MESH: X-Ray Diffraction ,MESH: Angiotensin-Converting Enzyme Inhibitors ,MESH: Infarction, Middle Cerebral Artery ,[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ,MESH: Macromolecular Substances ,General Medicine ,MESH: Male ,0104 chemical sciences ,Solvent ,Crystallography ,MESH: Angioneurotic Edema ,Chemical physics ,MESH: Dexamethasone ,Solvents ,MESH: Acute Disease ,MESH: Benzazepines ,MESH: Histamine Antagonists ,Constant (mathematics) ,Ribosomes ,MESH: Ribosomes ,Macromolecule - Abstract
International audience; The estimation of the bulk-solvent contribution to the diffraction of a macromolecular crystal makes use of a solvent mask which delimits the bulk-solvent regions in the crystal. It is shown that the way this mask is usually defined in CNS contains a bias which can lead to absurd results in the case of very large structures, where the calculations can only be made on relatively coarse grids. A modified procedure is described and applied to 70S ribosome data at 5.5 A resolution. The B factor affecting the bulk solvent is also discussed. Even in this case of very high and widely variable atomic B factors, it seems sufficient to consider a constant and isotropic B factor for the bulk solvent. This is initially set to the average value of the atomic B factor, but can be refined.
- Published
- 2005
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