Abstract
Crystallographic resolution is a key characteristic of diffraction data and represents one of the first decisions an experimenter has to make in data evaluation. Conservative approaches to the high-resolution cutoff determination are based on a number of criteria applied to the processed X-ray diffraction data only. However, high-resolution data that are weaker than arbitrary cutoffs can still result in the improvement of electron-density maps and refined structure models. Therefore, the impact of reflections from resolution shells higher than those previously used in conservative structure refinement should be analysed by the paired refinement protocol. For this purpose, a tool called PAIREF was developed to provide automation of this protocol. As a new feature, a complete cross-validation procedure has also been implemented. Here, the design, usage and control of the program are described, and its application is demonstrated on six data sets. The results prove that the inclusion of high-resolution data beyond the conventional criteria can lead to more accurate structure models.
Highlights
Crystallographic resolution is understood as the minimum plane spacing given by Bragg’s law for a particular set of X-ray diffraction intensities that are included in the structure analysis (Online Dictionary of Crystallography, https:// dictionary.iucr.org/Resolution)
TL: (d) differences in the overall R values; resolution shells with a width of 0.10 Awere added stepwise. (e) Comparison of CC* and CCwork of the refined models. ( f ) Rgap calculated using data up to 1.80 Adepending on the high-resolution cutoff; resolution shells with a width of 0.01 Awere added stepwise
cysteine dioxygenase from Rattus norvegicus (CDO): (g) differences in the overall R values; resolution shells with a width of 0.10 Awere added stepwise. (h) Comparison of CC* and CCfree of the model refined at 1.42 A, averaged over all of the 20 free sets
Summary
Crystallographic resolution is understood as the minimum plane spacing given by Bragg’s law for a particular set of X-ray diffraction intensities that are included in the structure analysis (Online Dictionary of Crystallography, https:// dictionary.iucr.org/Resolution). The resolution of data is limited due to a decrease in the intensity-to-noise ratio of reflections with the resolution. Conservative criteria were applied to estimate the resolution of crystallographic data. These criteria were based on a user-defined value of data quality indicators such as the signal-to-noise ratio hI/(I)i, the disagreement residual of multiple observations Rmerge, etc. The application of strict cutoff values on selected data quality indicators has been shown to be an obsolete approach
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