Literature DB >> 24531460

Weak data do not make a free lunch, only a cheap meal.

Zhipu Luo1, Kanagalaghatta Rajashankar2, Zbigniew Dauter1.   

Abstract

Four data sets were processed at resolutions significantly exceeding the criteria traditionally used for estimating the diffraction data resolution limit. The analysis of these data and the corresponding model-quality indicators suggests that the criteria of resolution limits widely adopted in the past may be somewhat conservative. Various parameters, such as Rmerge and I/σ(I), optical resolution and the correlation coefficients CC1/2 and CC*, can be used for judging the internal data quality, whereas the reliability factors R and Rfree as well as the maximum-likelihood target values and real-space map correlation coefficients can be used to estimate the agreement between the data and the refined model. However, none of these criteria provide a reliable estimate of the data resolution cutoff limit. The analysis suggests that extension of the maximum resolution by about 0.2 Å beyond the currently adopted limit where the I/σ(I) value drops to 2.0 does not degrade the quality of the refined structural models, but may sometimes be advantageous. Such an extension may be particularly beneficial for significantly anisotropic diffraction. Extension of the maximum resolution at the stage of data collection and structure refinement is cheap in terms of the required effort and is definitely more advisable than accepting a too conservative resolution cutoff, which is unfortunately quite frequent among the crystal structures deposited in the Protein Data Bank.

Entities:  

Keywords:  data-quality criteria; diffraction data resolution limit; nominal resolution; optical resolution

Mesh:

Substances:

Year:  2014        PMID: 24531460      PMCID: PMC3940200          DOI: 10.1107/S1399004713026680

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


  17 in total

1.  Data-collection strategies.

Authors:  Z Dauter
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-10

2.  SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

Authors:  A A Vaguine; J Richelle; S J Wodak
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-01-01

3.  Phasing at resolution higher than the experimental resolution.

Authors:  Rocco Caliandro; Benedetta Carrozzini; Giovanni L Cascarano; Liberato De Caro; Carmelo Giacovazzo; Dritan Siliqi
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-04-20

4.  A modified ACORN to solve protein structures at resolutions of 1.7 A or better.

Authors:  Yao Jia-xing; M M Woolfson; K S Wilson; E J Dodson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-10-19

5.  Linking crystallographic model and data quality.

Authors:  P Andrew Karplus; Kay Diederichs
Journal:  Science       Date:  2012-05-25       Impact factor: 47.728

6.  Structure of the shiga-like toxin I B-pentamer complexed with an analogue of its receptor Gb3.

Authors:  H Ling; A Boodhoo; B Hazes; M D Cummings; G D Armstrong; J L Brunton; R J Read
Journal:  Biochemistry       Date:  1998-02-17       Impact factor: 3.162

7.  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

Review 8.  Scaling and assessment of data quality.

Authors:  Philip Evans
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-12-14

9.  Better models by discarding data?

Authors:  K Diederichs; P A Karplus
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-06-15

10.  How good are my data and what is the resolution?

Authors:  Philip R Evans; Garib N Murshudov
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-06-13
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  12 in total

1.  Structure of Chlamydomonas reinhardtii THB1, a group 1 truncated hemoglobin with a rare histidine-lysine heme ligation.

Authors:  Selena L Rice; Lauren E Boucher; Jamie L Schlessman; Matthew R Preimesberger; Jürgen Bosch; Juliette T J Lecomte
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2015-05-20       Impact factor: 1.056

2.  A public database of macromolecular diffraction experiments.

Authors:  Marek Grabowski; Karol M Langner; Marcin Cymborowski; Przemyslaw J Porebski; Piotr Sroka; Heping Zheng; David R Cooper; Matthew D Zimmerman; Marc André Elsliger; Stephen K Burley; Wladek Minor
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-10-28       Impact factor: 7.652

Review 3.  Collection of X-Ray Diffraction Data from Macromolecular Crystals.

Authors:  Zbigniew Dauter
Journal:  Methods Mol Biol       Date:  2017

Review 4.  Assessing and maximizing data quality in macromolecular crystallography.

Authors:  P Andrew Karplus; Kay Diederichs
Journal:  Curr Opin Struct Biol       Date:  2015-07-24       Impact factor: 6.809

5.  Albumin-Based Transport of Nonsteroidal Anti-Inflammatory Drugs in Mammalian Blood Plasma.

Authors:  Mateusz P Czub; Katarzyna B Handing; Barat S Venkataramany; David R Cooper; Ivan G Shabalin; Wladek Minor
Journal:  J Med Chem       Date:  2020-06-17       Impact factor: 7.446

Review 6.  The solvent component of macromolecular crystals.

Authors:  Christian X Weichenberger; Pavel V Afonine; Katherine Kantardjieff; Bernhard Rupp
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-04-30

7.  A critical base pair in k-turns that confers folding characteristics and correlates with biological function.

Authors:  Scott A McPhee; Lin Huang; David M J Lilley
Journal:  Nat Commun       Date:  2014-10-29       Impact factor: 14.919

8.  Tackling the crystallographic structure determination of the COP9 signalosome.

Authors:  Richard D Bunker
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-03-01       Impact factor: 7.652

9.  Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining.

Authors:  Zbigniew Dauter; Alexander Wlodawer; Wladek Minor; Mariusz Jaskolski; Bernhard Rupp
Journal:  IUCrJ       Date:  2014-04-14       Impact factor: 4.769

10.  Solving the RNA polymerase I structural puzzle.

Authors:  María Moreno-Morcillo; Nicholas M I Taylor; Tim Gruene; Pierre Legrand; Umar J Rashid; Federico M Ruiz; Ulrich Steuerwald; Christoph W Müller; Carlos Fernández-Tornero
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-09-27
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