Editing X-ray crystallography (section)

=== Crystal symmetry, unit cell, and image scaling ===
{{further|Space group}}

The recorded series of two-dimensional diffraction patterns, each corresponding to a different crystal orientation, is converted into a three-dimensional set. Data processing begins with ''indexing'' the reflections. This means identifying the dimensions of the unit cell and which image peak corresponds to which position in reciprocal space. A byproduct of indexing is to determine the symmetry of the crystal, i.e., its ''[[space group]]''. Some space groups can be eliminated from the beginning. For example, reflection symmetries cannot be observed in chiral molecules; thus, only 65 space groups of 230 possible are allowed for protein molecules which are almost always chiral. Indexing is generally accomplished using an ''autoindexing'' routine.<ref>{{cite journal |vauthors=Powell HR |date=October 1999 |title=The Rossmann Fourier autoindexing algorithm in MOSFLM |journal=Acta Crystallographica. Section D, Biological Crystallography |volume=55 |issue=Pt 10 |pages=1690–1695 |bibcode=1999AcCrD..55.1690P |doi=10.1107/S0907444999009506 |pmid=10531518 |doi-access=free}}</ref> Having assigned symmetry, the data is then ''integrated''. This converts the hundreds of images containing the thousands of reflections into a single file, consisting of (at the very least) records of the [[Miller index]] of each reflection, and an intensity for each reflection (at this state the file often also includes error estimates and measures of partiality (what part of a given reflection was recorded on that image)).

A full data set may consist of hundreds of separate images taken at different orientations of the crystal. These have to be merged and scaled using peaks that appear in two or more images (''merging'') and scaling so there is a consistent intensity scale. Optimizing the intensity scale is critical because the relative intensity of the peaks is the key information from which the structure is determined. The repetitive technique of crystallographic data collection and the often high symmetry of crystalline materials cause the diffractometer to record many symmetry-equivalent reflections multiple times. This allows calculating the symmetry-related [[R-factor (crystallography)|R-factor]], a reliability index based upon how similar are the measured intensities of symmetry-equivalent reflections,{{clarify|date=February 2015}} thus assessing the quality of the data.