In-house sulfur SAD phasing: a case study of the effects of data quality and resolution cutoffs.
Single-wavelength anomalous diffraction (SAD) utilizing the weak signal of inherently present S atoms can be successfully used to solve macromolecular structures, although this is mostly performed with data from a synchrotron rather than a laboratory source. Using high redundancy, sufficiently accurate anomalous data may now often be collected in the laboratory using Cu Kalpha X-ray radiation. Systematic analyses of a laboratory-derived data set illuminate the effects of data quality, redundancy and resolution cutoffs on the ability to locate the S atoms and phase the structure of Ptr ToxA, a 13.2 kDa toxin secreted by the fungus Pyrenophora tritici-repentis. Three sulfurs contributed to the successful phasing of the structure and were located using the program SHELXD. It is observed that data quality improves with increasing redundancy, but after a certain point becomes worse owing to crystal decay, so that there is an optimal amount of data to include for the sulfur substructure solution. Further, the success rate in locating S atoms is dramatically improved at lower resolutions and in a manner similar to data quality, there exists an optimal resolution at which the likelihood of solving the substructure is maximized. Based on these observations, a strategy for SAD data collection and substructure solution is suggested.
Sarma
Ganapathy N
GN
Department of Biochemistry and Biophysics, 2011 ALS, Oregon State University, Corvallis, OR 97331, USA.
Karplus
P Andrew
PA
D003460:Crystallization; D018360:Crystallography, X-Ray / Q000379:methods*; D005656:Fungal Proteins / Q000737:chemistry*; D008958:Models, Molecular; D009183:Mycotoxins / Q000737:chemistry*; D011487:Protein Conformation; D012542:Scattering, Radiation; D013455:Sulfur / Q000737:chemistry*
D005656:Fungal Proteins; D009183:Mycotoxins; C105776:TOXA protein, Pyrenophora tritici-repentis; D013455:Sulfur