HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes.

By Wladek Minor, M. Cymborowski, Zbyszek Otwinowski, M. Chruszcz. 2006

1,985 citations recorded by the source corpus.

A new approach that integrates data collection, data reduction, phasing and model building significantly accelerates the process of structure determination and on average minimizes the number of data sets and synchrotron time required for structure solution. Initial testing of the HKL-3000 system (the beta version was named HKL-2000_ph) with more than 140 novel structure determinations has proven its high value for MAD/SAD experiments. The heuristics for choosing the best computational strategy at different data resolution limits of phasing signal and crystal diffraction are being optimized. The typical end result is an interpretable electron-density map with a partially built structure and, in some cases, an almost complete refined model. The current development is oriented towards very fast structure solution in order to provide feedback during the diffraction experiment. Work is also proceeding towards improving the quality of phasing calculation and model building.

Subfields: Materials Chemistry

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

Citations in the corpus

Neutron diffraction studies towards deciphering the protonation state of catalytic residues in the bacterial KDN9P phosphatase. (2013, methodology): “The intensities of the reflections were integrated and scaled with DENZO (v.1.96.2) and SCALEPACK (v.1.98.2) (Otwinowski & Minor, 1997; Minor et al., 2006).”
Structural and Biophysical Studies of the Human IL-7/IL-7Rα Complex (2009, methodology): “X-ray data were collected at the Structural Biology Center 19ID beamline, Advanced Photon Source, Argonne National Laboratories, Chicago, IL, USA and processed using HKL-3000 (Minor et al., 2006).”
The Phenix Software for Automated Determination of Macromolecular Structures (2011, methodology): “Finally, many of the automated methods have been brought together in automated structure solution pipelines such as AutoRickshaw[12], HKL3000[13], Crank[14] and AutoSHARP[15] plus AutoBUSTER[16].”
Structural basis for cooperative function of Mettl3 and Mettl14 methyltransferases (2016, neutral): “Data were indexed, integrated, and scaled by the program HKL3000 (Minor et al., 2006).”
Neutron Crystal Structure of RAS GTPase Puts in Question the Protonation State of the GTP γ-Phosphate* (2015, methodology): “The diffraction data were indexed, integrated, and scaled using the HKL-3000 software suite (42).”
Cyclic GMP-AMP Containing Mixed Phosphodiester Linkages Is An Endogenous High Affinity Ligand for STING (2013, positive): “The data were integrated and scaled with HKL3000 package (Minor et al., 2006).”
A public database of macromolecular diffraction experiments. (2016, methodology): “In some cases, new functionality was developed within the HKL-2000/HKL-3000 suite to permit the automatic execution of some program 1184 Grabowski et al. A public database of macromolecular diffraction experiments Acta Cryst.”
Structural and immunologic characterization of bovine, horse, and rabbit serum albumins (2012, methodology): “All structures were solved using HKL-3000 (Minor et al., 2006) coupled with MOLREP (Vagin and Teplyakov, 1997).”