Semi-automatic Structure Solution with HKL-3000
MINOR W.1, CYMBOROWSKI M.1 , OTWINOWSKI Z.2, BOREK D.2,
1
University of Virginia, Charlottesville, VA, 22908-0736, USA 2UT Southwestern Medical
Center at Dallas, Midwest Center for Structural Genomics
HKL-3000 integrates data collection, data reduction, phasing, and model building to
significantly accelerate the process of structure determination and on average minimize the
number of data sets and crystals required for structure solution. In its execution it merges
several modules and software applications into the structure determination pipeline: an
experiment control module for some beamlines and instruments, data reduction module,
phasing by SAD/MAD or molecular replacement, fast model building, and initial
refinement. The system is being developed and tested in the high-throughput environment
of the Midwest Center for Structural Genomics. The robustness of HKL-3000 has
improved considerably over time and currently over 650 structures were determined with
it.
The continuous advancement of the decision-making procedures within HKL-3000 made it
a system of choice for MCSG projects. A very quick path of 10–15 min from raw images
to solved structure with 70% of a model built is no longer a surprise, but is a routine
operation for data that diffract to 2.5 Ǻ or better. The experience with hundreds of
structures determined by experimental phasing helped us to establish rules for the best
approach to structure determination when the available data are in three categories:
unsolvable with current data, borderline and easy. Current work concentrates on improving
the approach to borderline cases of structure determination rather than optimizing
intermediate calculations for easy cases, thus shifting borderline cases into the easy
category and unsolvable into borderline.
The data provided to tutorial workshop participants will be used to show that a surprisingly
small fraction of experimental information is sufficient for the project to succeed. An
important implication is that simple experimental protocols are sufficient in most cases and
they even may be optimal for the most challenging ones. Feedback from fast preliminary
structure solutions proved to be one of the critical components of success. We expect also
to solve structures provided by workshop participants.
References
Minor W, Cymborowski M, Otwinowski Z, Chruszcz M (2006) Acta Crystallographica
Section D: Biological Crystallography 62: 859-66.
Kirillova O, Chruszcz M, Shumilin IA, Skarina T, Gorodichtchenskaia E, Cymborowski
M, Savchenko A, Edwards A, Minor W (2007) Acta Crystallographica Section D:
Biological Crystallography 63: 348-54.
Otwinowski Z, Borek D, Majewski W, Minor W (2003) Acta Crystallographica. Section
A: Foundations of Crystallography 59: 228-34.
Zheng H, Chruszcz M, Lasota P, Lebioda L, Minor W (2008) Journal of Inorganic
Biochemistry 102(9): 1765-76.
Chruszcz M, Wlodawer A, Minor W (2008) Biophysical Journal 95(1): 1-9.
Wlodawer A, Minor W, Dauter Z, Jaskolski M (2008) Febs Journal 275: 1-21.
Otwinowski Z, Minor W (1997) Methods in Enzymology 275: 307-326.