How does the age of a crystal affect X-Ray diffraction data?
Reading and References:
The Crystal Structure of Yeast Phenylalanine tRNA at 2.0 Å Resolution: Cleavage by Mg2+ in 15-year Old Crystals.
Luca Jovine, Snezana Djordjevic and Daniela Rhodes. Journal of Molecular Biology. Volume 301, Issue 2, 11 August 2000, Pages 401-414. https://doi.org/10.1006/jmbi.2000.3950
Abstract: We have re-determined the crystal structure of yeast tRNAPhe to 2.0 Å resolution using 15 year old crystals. The accuracy of the new structure, due both to higher resolution data and formerly unavailable refinement methods, consolidates the previous structural information, but also reveals novel details. In particular, the water structure around the tightly bound Mg2+ is now clearly resolved, and hence provides more accurate information on the geometry of the magnesium-binding sites and the role of water molecules in coordinating the metal ions to the tRNA. We have assigned a total of ten magnesium ions and identified a partly conserved geometry for high-affinity Mg2+ binding. In the electron density map there is also clear density for a spermine molecule binding in the major groove of the TΨC arm and also contacting a symmetry-related tRNA molecule. Interestingly, we have also found that two specific regions of the tRNA in the crystals are partially cleaved. The sites of hydrolysis are within the D and anticodon loops in the vicinity of Mg2+.
Atomic Resolution Structure of a Succinimide Intermediate in E. coli CheY.
Miljan Simonovic and Karl Volz. Journal of Molecular Biology. Volume 322, Issue 4, 27 September 2002, Pages 663-667. https://doi.org/10.1016/S0022-2836(02)00821-5
Abstract: Isomerization of aspartate to isoaspartate occurs spontaneously in proteins, causes changes in protein structures, and correlates positively with the aging processes of many organisms, including Alzheimer disease in humans. Aspartate isomerization proceeds through an unstable cyclic succinimide intermediate. There are few protein structure determinations that have characterized the intermediates and products of this isomerization reaction. Here we report the discovery of an unusually stabilized succinimide ring in the 1.1 Å structure of the Escherichia coli CheY protein, as determined from a crystal eight years old. The ring is formed by the side-chain of aspartate 75 and the backbone nitrogen of glycine 76 in an exposed loop of the molecule. Stabilization of the succinimide is through interaction of a sulfate ion oxygen atom with the imide nitrogen atom. Formation of the ring caused conformational changes in the loop, but did not alter the overall structure of the protein.
Using rational screening and electron microscopy to optimize the crystallization of succinate:ubiquinone oxidoreductase from Escheria coli.
Rob Horsefield, Victoria Yankovskaya, Susanna Törnroth, César Luna-Chavez, Elizabeth Stambouli, James Barber, Bernadette Byrne, Gary Cecchini and So Iwata. Acta Crystallographica Section D. Volume 59, Part 3, March 2003, Pages 600-602. https://doi.org/10.1107/S0907444903002075
Abstract: The membrane-bound respiratory complex II, succinate:ubiquinone oxidoreductase (SQR) from Escherichia coli, has been anaerobically expressed, then purified and crystallized. The initial crystals obtained were small and diffracted poorly. In order to facilitate structure determination, rational screening and sample-quality analysis using electron microscopy was implemented. The crystals of SQR from E. coli belong to the trigonal space group R32, with unit-cell parameters a = b = 138.7, c = 521.9 Å, and diffract to 2.6 Å resolution. The optimization strategy used for obtaining well diffracting SQR crystals is applicable to a wide range of membrane proteins.
From the Results and Discussion section of the publication: "It proved critical to freeze the crystals within 72 h of crystallization set-up. Crystals that were frozen after this time limit showed no diffraction. This alteration in properties was apparent by the change in colour from deep orange to pale yellow that was observed in crystals more than four weeks old (Fig. 1 c). The deep orange colour of the crystals is attributed to the presence of haem b within the protein. The loss or breakdown of haem, demonstrated by the change of colour in the crystals, could lead to structural instability and consequently loss of diffraction."