Editing X-ray crystallography (section)

===Data collection===

====Mounting the crystal====
[[File:Kappa goniometer animation.ogg|thumb|left|Animation showing the five motions possible with a four-circle kappa goniometer. The rotations about each of the four angles φ, κ, ω and 2θ leave the crystal within the X-ray beam, but change the crystal orientation. The detector (red box) can be slid closer or further away from the crystal, allowing higher resolution data to be taken (if closer) or better discernment of the Bragg peaks (if further away).]]

The crystal is mounted for measurements so that it may be held in the X-ray beam and rotated. There are several methods of mounting. In the past, crystals were loaded into glass capillaries with the crystallization solution (the [[mother liquor]]).  Crystals of small molecules are typically attached with oil or glue to a glass fiber or a loop, which is made of nylon or plastic and attached to a solid rod.  Protein crystals are scooped up by a loop, then flash-frozen with [[liquid nitrogen]].<ref>{{cite book | vauthors = Jeruzalmi D | title = Macromolecular Crystallography Protocols, Volume 2 | chapter = First analysis of macromolecular crystals: biochemistry and x-ray diffraction | series = Methods in Molecular Biology | volume = 364|pages=43–62 | date = 2006 | pmid = 17172760 | doi = 10.1385/1-59745-266-1:43 | isbn = 1-59745-266-1 }}</ref> This freezing reduces the radiation damage of the X-rays, as well as thermal motion (the Debye-Waller effect). However, untreated protein crystals often crack if flash-frozen; therefore, they are generally pre-soaked in a cryoprotectant solution before freezing.<ref>{{cite journal | vauthors = Helliwell JR | title = Protein crystal perfection and its application | journal = Acta Crystallographica. Section D, Biological Crystallography | volume = 61 | issue = Pt 6 | pages = 793–798 | date = June 2005 | pmid = 15930642 | doi = 10.1107/S0907444905001368 | bibcode = 2005AcCrD..61..793H | author-link = John R. Helliwell | doi-access = free }}</ref> This pre-soak may itself cause the crystal to crack, ruining it for crystallography. Generally, successful cryo-conditions are identified by trial and error.{{cn|date=July 2024}}

The capillary or loop is mounted on a [[goniometer]], which allows it to be positioned accurately within the X-ray beam and rotated. Since both the crystal and the beam are often very small, the crystal must be centered within the beam to within ~25 micrometers accuracy, which is aided by a camera focused on the crystal. The most common type of goniometer is the "kappa goniometer", which offers three angles of rotation: the ω angle, which rotates about an axis perpendicular to the beam; the κ angle, about an axis at ~50° to the ω axis; and, finally, the φ angle about the loop/capillary axis. When the κ angle is zero, the ω and φ axes are aligned. The κ rotation allows for convenient mounting of the crystal, since the arm in which the crystal is mounted may be swung out towards the crystallographer. The oscillations carried out during data collection (mentioned below) involve the ω axis only. An older type of goniometer is the four-circle goniometer, and its relatives such as the six-circle goniometer.{{cn|date=July 2024}}

==== Recording the reflections ====
[[File:X-ray diffraction pattern 3clpro.jpg|thumb|An X-ray diffraction pattern of a crystallized enzyme. The pattern of spots (''reflections'') and the relative strength of each spot (''intensities'') can be used to determine the structure of the enzyme.]]
The relative intensities of the reflections provides information to determine the arrangement of molecules within the crystal in atomic detail. The intensities of these reflections may be recorded with [[photographic film]], an area detector (such as a [[hybrid pixel detector|pixel detector]]) or with a [[charge-coupled device]] (CCD) image sensor. The peaks at small angles correspond to low-resolution data, whereas those at high angles represent high-resolution data; thus, an upper limit on the eventual resolution of the structure can be determined from the first few images. Some measures of diffraction quality can be determined at this point, such as the [[mosaicity]] of the crystal and its overall disorder, as observed in the peak widths. Some pathologies of the crystal that would render it unfit for solving the structure can also be diagnosed quickly at this point.{{cn|date=July 2024}}

One set of spots is insufficient to reconstruct the whole crystal; it represents only a small slice of the full three dimensional set. To collect all the necessary information, the crystal must be rotated step-by-step through 180°, with an image recorded at every step; actually, slightly more than 180° is required to cover [[reciprocal space]], due to the curvature of the [[Ewald sphere]]. However, if the crystal has a higher symmetry, a smaller angular range such as 90° or 45° may be recorded. The rotation axis should be changed at least once, to avoid developing a "blind spot" in reciprocal space close to the rotation axis. It is customary to rock the crystal slightly (by 0.5–2°) to catch a broader region of reciprocal space.{{cn|date=July 2024}}

Multiple data sets may be necessary for certain [[Phase problem|phasing]] methods. For example, [[multi-wavelength anomalous dispersion]] phasing requires that the scattering be recorded at least three (and usually four, for redundancy) wavelengths of the incoming X-ray radiation. A single crystal may degrade too much during the collection of one data set, owing to radiation damage; in such cases, data sets on multiple crystals must be taken.<ref>{{cite journal |vauthors=Ravelli RB, Garman EF |date=October 2006 |title=Radiation damage in macromolecular cryocrystallography |journal=Current Opinion in Structural Biology |volume=16 |issue=5 |pages=624–629 |doi=10.1016/j.sbi.2006.08.001 |pmid=16938450}}</ref>