Literature DB >> 10531526

Detecting outliers in non-redundant diffraction data.

R J Read1.   

Abstract

Outliers are observations which are very unlikely to be correct, as judged by independent observations or other prior information. Such unexpected observations are treated, effectively, as being more informative about possible models, so they can seriously impede the course of structure determination and refinement. The best way to detect and eliminate outliers is to collect highly redundant data, but it is not always possible to make multiple measurements of every reflection. For non-redundant data, the prior expectation given either by a Wilson distribution of intensities or model-based structure-factor probability distributions can be used to detect outliers. This captures mostly the excessively strong reflections, which dominate the features of electron-density maps or, even more so, Patterson maps. The outlier rejection tests have been implemented in a program, Outliar.

Mesh:

Year:  1999        PMID: 10531526     DOI: 10.1107/s0907444999008471

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  11 in total

1.  Determining Rieske cluster reduction potentials.

Authors:  Eric N Brown; Rosmarie Friemann; Andreas Karlsson; Juan V Parales; Manon M-J Couture; Lindsay D Eltis; S Ramaswamy
Journal:  J Biol Inorg Chem       Date:  2008-08-22       Impact factor: 3.358

2.  Autoindexing with outlier rejection and identification of superimposed lattices.

Authors:  Nicholas K Sauter; Billy K Poon
Journal:  J Appl Crystallogr       Date:  2010-04-30       Impact factor: 3.304

3.  PHENIX: a comprehensive Python-based system for macromolecular structure solution.

Authors:  Paul D Adams; Pavel V Afonine; Gábor Bunkóczi; Vincent B Chen; Ian W Davis; Nathaniel Echols; Jeffrey J Headd; Li-Wei Hung; Gary J Kapral; Ralf W Grosse-Kunstleve; Airlie J McCoy; Nigel W Moriarty; Robert Oeffner; Randy J Read; David C Richardson; Jane S Richardson; Thomas C Terwilliger; Peter H Zwart
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-01-22

4.  phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics.

Authors:  Pavel V Afonine; Ralf W Grosse-Kunstleve; Vincent B Chen; Jeffrey J Headd; Nigel W Moriarty; Jane S Richardson; David C Richardson; Alexandre Urzhumtsev; Peter H Zwart; Paul D Adams
Journal:  J Appl Crystallogr       Date:  2010-05-22       Impact factor: 3.304

5.  Using SAD data in Phaser.

Authors:  Randy J Read; Airlie J McCoy
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-03-05

6.  A new generation of crystallographic validation tools for the protein data bank.

Authors:  Randy J Read; Paul D Adams; W Bryan Arendall; Axel T Brunger; Paul Emsley; Robbie P Joosten; Gerard J Kleywegt; Eugene B Krissinel; Thomas Lütteke; Zbyszek Otwinowski; Anastassis Perrakis; Jane S Richardson; William H Sheffler; Janet L Smith; Ian J Tickle; Gert Vriend; Peter H Zwart
Journal:  Structure       Date:  2011-10-12       Impact factor: 5.006

7.  Towards automated crystallographic structure refinement with phenix.refine.

Authors:  Pavel V Afonine; Ralf W Grosse-Kunstleve; Nathaniel Echols; Jeffrey J Headd; Nigel W Moriarty; Marat Mustyakimov; Thomas C Terwilliger; Alexandre Urzhumtsev; Peter H Zwart; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-03-16

8.  A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error.

Authors:  Randy J Read; Airlie J McCoy
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-03-01       Impact factor: 7.652

9.  Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations.

Authors:  Susan E Tsutakawa; Altaf H Sarker; Clifford Ng; Andrew S Arvai; David S Shin; Brian Shih; Shuai Jiang; Aye C Thwin; Miaw-Sheue Tsai; Alexandra Willcox; Mai Zong Her; Kelly S Trego; Alan G Raetz; Daniel Rosenberg; Albino Bacolla; Michal Hammel; Jack D Griffith; Priscilla K Cooper; John A Tainer
Journal:  Proc Natl Acad Sci U S A       Date:  2020-06-10       Impact factor: 11.205

10.  SIMBAD: a sequence-independent molecular-replacement pipeline.

Authors:  Adam J Simpkin; Felix Simkovic; Jens M H Thomas; Martin Savko; Andrey Lebedev; Ville Uski; Charles Ballard; Marcin Wojdyr; Rui Wu; Ruslan Sanishvili; Yibin Xu; María Natalia Lisa; Alejandro Buschiazzo; William Shepard; Daniel J Rigden; Ronan M Keegan
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-06-08       Impact factor: 7.652

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