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

Journal Article · · Acta Crystallographica. Section D: Biological Crystallography (Online)

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 asRmergeandI/σ(I), optical resolution and the correlation coefficients CC1/2and CC*, can be used for judging the internal data quality, whereas the reliability factorsRandRfreeas 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 theI/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.

Research Organization:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Organization:
National Institutes of Health (NIH)
OSTI ID:
1133204
Journal Information:
Acta Crystallographica. Section D: Biological Crystallography (Online), Vol. 70, Issue 2; ISSN 1399-0047
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
ENGLISH

References (23)

On the use of the merging R factor as a quality indicator for X-ray data journal April 1997
Linking Crystallographic Model and Data Quality journal May 2012
How good are my data and what is the resolution? journal June 2013
Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures: Protein crystallography for non-crystallographers journal November 2007
Structure of the type I L -asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii at 2.16 Å resolution journal February 2005
Structural Analysis of a Putative Aminoglycoside N-Acetyltransferase from Bacillus anthracis journal July 2011
A short history of SHELX journal December 2007
Resolution revisited: limit of detail in electron density maps journal May 1984
Improved R-factors for diffraction data analysis in macromolecular crystallography journal April 1997
Ab initio determination of the crystal structure of cytochrome c6 and comparison with plastocyanin journal November 1995
Phasing at resolution higher than the experimental resolution journal April 2005
The Protein Data Bank journal January 2000
Data-collection strategies journal October 1999
Scaling and assessment of data quality journal December 2005
Structure of the Shiga-like Toxin I B-Pentamer Complexed with an Analogue of Its Receptor Gb 3 , journal February 1998
REFMAC 5 for the refinement of macromolecular crystal structures journal March 2011
[20] Processing of X-ray diffraction data collected in oscillation mode book January 1997
Structure of the single-stranded DNA-binding protein SSB from Thermus aquaticus journal October 2006
SFCHECK : a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model journal January 1999
Global indicators of X-ray data quality journal April 2001
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
False detail in three-dimensional Fourier representations of crystal structures journal July 1948
Better models by discarding data? journal June 2013

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