Measuring and using information gained by observing diffraction data.

Acta Crystallographica. Section D, Structural Biology
R J ReadAirlie J McCoy

Abstract

The information gained by making a measurement, termed the Kullback-Leibler divergence, assesses how much more precisely the true quantity is known after the measurement was made (the posterior probability distribution) than before (the prior probability distribution). It provides an upper bound for the contribution that an observation can make to the total likelihood score in likelihood-based crystallographic algorithms. This makes information gain a natural criterion for deciding which data can legitimately be omitted from likelihood calculations. Many existing methods use an approximation for the effects of measurement error that breaks down for very weak and poorly measured data. For such methods a different (higher) information threshold is appropriate compared with methods that account well for even large measurement errors. Concerns are raised about a current trend to deposit data that have been corrected for anisotropy, sharpened and pruned without including the original unaltered measurements. If not checked, this trend will have serious consequences for the reuse of deposited data by those who hope to repeat calculations using improved new methods.

References

Jun 24, 2004·Acta Crystallographica. Section D, Biological Crystallography·Airlie J McCoyRandy J Read
May 13, 2006·Proceedings of the National Academy of Sciences of the United States of America·Michael StrongDavid Eisenberg
Dec 5, 2006·Nucleic Acids Research·Helen BermanJohn L Markley
Jan 1, 1997·Methods in Enzymology·R J Read
Aug 1, 2007·Journal of Applied Crystallography·Airlie J McCoyRandy J Read
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Martyn D WinnKeith S Wilson
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Garib N MurshudovAlexei A Vagin
May 26, 2012·Science·P Andrew Karplus, Kay Diederichs
Mar 10, 2016·Acta Crystallographica. Section D, Structural Biology·Randy J Read, Airlie J McCoy
Mar 23, 2017·Proceedings of the National Academy of Sciences of the United States of America·Airlie J McCoyRandy J Read
Apr 6, 2019·Acta Crystallographica. Section D, Structural Biology·Mostafa JamshidihaRandy J Read
Jan 8, 2020·Acta Crystallographica. Section D, Structural Biology·Kaushik S HattiRandy J Read

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Citations

Aug 4, 2020·Acta Crystallographica. Section D, Structural Biology·Logan S RichardsJose A Rodriguez

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Methods Mentioned

BETA
single-crystal diffraction

Software Mentioned

Phaser
CTRUNCATE
Mathematica
phasertng
UCLA Diffraction Anisotropy Server
STARANISO

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