Section 18.1.6. Data

Resolution, accuracy, completeness and weighting of data all have an impact on the refinement process. Small-molecule crystals usually, but not always, diffract to well beyond atomic resolution. Macromolecular crystals do not generally diffract to atomic resolution. Macromolecular structures are by definition large, which in turn means that the unit cells are large and the number of diffracting unit cells per crystal is small when compared to small-molecule crystals of similar size. Fortunately, the situation can be partially offset with the use of the much more intense radiation generated by synchrotrons (Part 8 ) and by improved data-collection methods (Parts 7 –11 ). Synchrotron-radiation sources designed to produce intense beams of X-rays for the study of materials are becoming much more readily available. As a consequence, both higher resolution and statistically better data can be obtained. Improvements in area-detector technology, protein purification, cryocrystallography and data-integration software beneficially influence the refinement process.

Refinement of crystal structures is a statistical process. There is no substitute for adequate amounts of accurate, correctly weighted data. Lower accuracy can be accommodated by increased amounts of data and correct weighting. Unfortunately, determining the correct weighting for macromolecular diffraction data is difficult. Maximum-likelihood methods are more robust than least-squares methods against improperly weighted data.

It has been clearly demonstrated that the best procedure for refining small molecules is to include all of the observations as integrated intensities, properly weighted, without preliminary symmetry averaging. Inclusion of weak data and refinement on diffracted intensity does not change the results very much, but has a strong effect on the precision of the parameter estimates derived from the refinement.

The long-standing debate as to whether refinement should be against structure-factor amplitudes or diffracted intensity has been resolved for small-molecule crystallography. Refinement against intensity is preferred because it is closer to the experimentally observed quantity, and the statistical weighting of the data is superior to that obtained for structure-factor amplitudes. If the model is correct and the data are reasonably good, the primary distinction between the two approaches is in the standard uncertainties of the derived parameters, which are usually somewhat better if the refinement is against diffracted intensity.