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

Abstract

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 electrondensity 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.

Atomic resolution structure of the cytoplasmic domain of Yersinia pestis YscU, a regulatory switch involved in type III secretion

“…A SAD data set was collected on a single YscU N263A/P264A crystal soaked with bromide using the peak wavelength set at 0.91957 Å. X-ray diffraction data from a single YscUcleaved crystal soaked with iodide was collected at 1.5418 Å wavelength with a MAR345 image plate detector mounted on a Rigaku RU-H3R generator operated at 50 kV and 100 mA (Rigaku Corporation, The Woodlands, TX). All data sets were processed with the HKL3000 program suite 24 and the processed data were submitted into the SGXPRO program platform for automatic structure solution. 25 The YscU N263A/ P264A structure was solved by locating eight bromide ions in the asymmetric unit with data extending to 1.96 Å using SHELXD 26 and the handedness was subsequently determined by ISAS.…”

Structures of open (R) and close (T) states of prephenate dehydratase (PDT)—Implication of allosteric regulation by l-phenylalanine

“…After density modification (DM) (1994), partial models of 206 residues (Sa-PDT) or 338 residues (Ct-PDT) without side chains were obtained from automatic model building trials using the program RESOLVE (Terwilliger, 2003). All of the above programs are integrated within the program suite HKL-3000 (Minor et al, 2006). From the initial partial models, each PDT structure was manually built using the program COOT (Emsley and Cowtan, 2004).…”

“…The data set was cut off at 2.3Å with completeness of 53% and I/σ of about 5.8. All diffraction data were processed and scaled with HKL3000 suite (Table 1) (Minor et al, 2006).…”

Crystal structures of TM0549 and NE1324—two orthologs of E. coli AHAS isozyme III small regulatory subunit

“…Data from Se-Met substituted samples were processed with HKL-2000 (Otwinowski and Minor 1997). Structures were solved using SAD data, and initial models were built with HKL-3000 (Minor et al 2006), which is integrated with SHELXD (Schneider and Sheldrick 2002), SHELXE (Sheldrick 2002), MLPHARE (Otwinowski 1991), DM (Cowtan 1994), O (Jones et al 1991), SOLVE (Terwilliger and Berendzen 1999), and RESOLVE (Terwilliger 2002). Initial models were refined with REFMAC5 (Murshudov et al 1997) and COOT (Emsley and Cowtan 2004).…”