Literature DB >> 18421130

Foundations of residual-density analysis.

Kathrin Meindl1, Julian Henn.   

Abstract

New and concise descriptors of the residual density are presented, namely the gross residual electrons, the net residual electrons and the fractal dimension distribution. These descriptors indicate how much residual density is present and in what way it is distributed, i.e. the extent to which the distribution is featureless. The amount of residual density present accounts for noise in the experimental data as well as for modeling inadequacies. Therefore, the minimization of the gross residual electrons during refinement serves as a quality criterion. In the case where only Gaussian noise is present in the residual density, the fractal distribution is parabolic in shape. Deviations from this shape therefore serve as an indicator for systematic errors. The new measures have been applied to simulated and experimental data in order to study the effects of noise, model inadequacies and truncation in the experimental resolution. These measures, although designed and examined with particular regard to applications of space residual density, are very general and can in principle also be applied to space and momentum residual densities in a one-, two-, three- or higher-dimensional Euclidean space.

Year:  2008        PMID: 18421130     DOI: 10.1107/S0108767308006879

Source DB:  PubMed          Journal:  Acta Crystallogr A        ISSN: 0108-7673            Impact factor:   2.290


  17 in total

1.  Systematic analysis of residual density suggests that a major limitation in well-refined X-ray structures of proteins is the omission of ordered solvent.

Authors:  Jimin Wang
Journal:  Protein Sci       Date:  2017-03-07       Impact factor: 6.725

2.  Accurate high-resolution single-crystal diffraction data from a Pilatus3 X CdTe detector.

Authors:  Lennard Krause; Kasper Tolborg; Thomas Bjørn Egede Grønbech; Kunihisa Sugimoto; Bo Brummerstedt Iversen; Jacob Overgaard
Journal:  J Appl Crystallogr       Date:  2020-04-23       Impact factor: 3.304

3.  Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature.

Authors:  Jan Kern; Roberto Alonso-Mori; Rosalie Tran; Johan Hattne; Richard J Gildea; Nathaniel Echols; Carina Glöckner; Julia Hellmich; Hartawan Laksmono; Raymond G Sierra; Benedikt Lassalle-Kaiser; Sergey Koroidov; Alyssa Lampe; Guangye Han; Sheraz Gul; Dörte Difiore; Despina Milathianaki; Alan R Fry; Alan Miahnahri; Donald W Schafer; Marc Messerschmidt; M Marvin Seibert; Jason E Koglin; Dimosthenis Sokaras; Tsu-Chien Weng; Jonas Sellberg; Matthew J Latimer; Ralf W Grosse-Kunstleve; Petrus H Zwart; William E White; Pieter Glatzel; Paul D Adams; Michael J Bogan; Garth J Williams; Sébastien Boutet; Johannes Messinger; Athina Zouni; Nicholas K Sauter; Vittal K Yachandra; Uwe Bergmann; Junko Yano
Journal:  Science       Date:  2013-02-14       Impact factor: 47.728

Review 4.  The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals.

Authors:  Sajesh P Thomas; Amol G Dikundwar; Sounak Sarkar; Mysore S Pavan; Rumpa Pal; Venkatesha R Hathwar; Tayur N Guru Row
Journal:  Molecules       Date:  2022-06-08       Impact factor: 4.927

5.  Experimental Electron Density and Neutron Diffraction Studies on the Polymorphs of Sulfathiazole.

Authors:  Ioana Sovago; Matthias J Gutmann; J Grant Hill; Hans Martin Senn; Lynne H Thomas; Chick C Wilson; Louis J Farrugia
Journal:  Cryst Growth Des       Date:  2014-01-17       Impact factor: 4.076

6.  Poly[diaquatris(μ6-4,6-dioxo-1,4,5,6-tetra-hydro-1,3,5-triazine-2-carboxylato)tripotassium].

Authors:  Sarra Soudani; Emmanuel Aubert; Emmanuel Wenger; Christian Jelsch; Isabelle Gautier-Luneau; Cherif Ben Nasr
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2014-04-09

7.  Relativistic Hirshfeld atom refinement of an organo-gold(I) compound.

Authors:  Sylwia Pawlędzio; Maura Malinska; Magdalena Woińska; Jakub Wojciechowski; Lorraine Andrade Malaspina; Florian Kleemiss; Simon Grabowsky; Krzysztof Woźniak
Journal:  IUCrJ       Date:  2021-05-26       Impact factor: 4.769

8.  The advanced treatment of hydrogen bonding in quantum crystallography.

Authors:  Lorraine A Malaspina; Alessandro Genoni; Dylan Jayatilaka; Michael J Turner; Kunihisa Sugimoto; Eiji Nishibori; Simon Grabowsky
Journal:  J Appl Crystallogr       Date:  2021-04-16       Impact factor: 3.304

9.  Charge density studies of multicentre two-electron bonding of an anion radical at non-ambient temperature and pressure.

Authors:  Valentina Milašinović; Krešimir Molčanov; Anna Krawczuk; Nikita E Bogdanov; Boris A Zakharov; Elena V Boldyreva; Christian Jelsch; Biserka Kojić-Prodić
Journal:  IUCrJ       Date:  2021-06-12       Impact factor: 4.769

10.  Location of Cu(2+) in CHA zeolite investigated by X-ray diffraction using the Rietveld/maximum entropy method.

Authors:  Casper Welzel Andersen; Martin Bremholm; Peter Nicolai Ravnborg Vennestrøm; Anders Bank Blichfeld; Lars Fahl Lundegaard; Bo Brummerstedt Iversen
Journal:  IUCrJ       Date:  2014-09-23       Impact factor: 4.769

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.