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Title: Development of Control Applications for High-Throughput Protein Crystallography Experiments

Abstract

An integrated client-server control system (PCCS) with a unified relational database (PCDB) has been developed for high-throughput protein crystallography experiments on synchrotron beamlines. The major steps in protein crystallographic experiments (purification, crystallization, crystal harvesting, data collection, and data processing) are integrated into the software. All information necessary for performing protein crystallography experiments is stored in the PCDB database (except raw X-ray diffraction data, which is stored in the Network File Server). To allow all members of a protein crystallography group to participate in experiments, the system was developed as a multi-user system with secure network access based on TCP/IP secure UNIX sockets. Secure remote access to the system is possible from any operating system with X-terminal and SSH/X11 (Secure Shell with graphical user interface) support. Currently, the system covers the high-throughput X-ray data collection stages and is being commissioned at BL5A and NW12A (PF, PF-AR, KEK, Tsukuba, Japan)

Authors:
; ; ; ; ; ; ;  [1]
  1. Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki (Japan)
Publication Date:
OSTI Identifier:
21043401
Resource Type:
Journal Article
Resource Relation:
Journal Name: AIP Conference Proceedings; Journal Volume: 879; Journal Issue: 1; Conference: 9. international conference on synchrotron radiation instrumentation, Daegu (Korea, Republic of), 28 May - 2 Jun 2006; Other Information: DOI: 10.1063/1.2436451; (c) 2007 American Institute of Physics; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; COMPUTER CODES; CONTROL; CONTROL SYSTEMS; CRYSTALLIZATION; CRYSTALLOGRAPHY; CRYSTALS; DATA PROCESSING; INTERFACES; JAPANESE ORGANIZATIONS; PROTEINS; SYNCHROTRON RADIATION; X RADIATION; X-RAY DIFFRACTION

Citation Formats

Gaponov, Yurii A., Matsugaki, Naohiro, Honda, Nobuo, Sasajima, Kumiko, Igarashi, Noriyuki, Hiraki, Masahiko, Yamada, Yusuke, and Wakatsuki, Soichi. Development of Control Applications for High-Throughput Protein Crystallography Experiments. United States: N. p., 2007. Web. doi:10.1063/1.2436451.
Gaponov, Yurii A., Matsugaki, Naohiro, Honda, Nobuo, Sasajima, Kumiko, Igarashi, Noriyuki, Hiraki, Masahiko, Yamada, Yusuke, & Wakatsuki, Soichi. Development of Control Applications for High-Throughput Protein Crystallography Experiments. United States. doi:10.1063/1.2436451.
Gaponov, Yurii A., Matsugaki, Naohiro, Honda, Nobuo, Sasajima, Kumiko, Igarashi, Noriyuki, Hiraki, Masahiko, Yamada, Yusuke, and Wakatsuki, Soichi. Fri . "Development of Control Applications for High-Throughput Protein Crystallography Experiments". United States. doi:10.1063/1.2436451.
@article{osti_21043401,
title = {Development of Control Applications for High-Throughput Protein Crystallography Experiments},
author = {Gaponov, Yurii A. and Matsugaki, Naohiro and Honda, Nobuo and Sasajima, Kumiko and Igarashi, Noriyuki and Hiraki, Masahiko and Yamada, Yusuke and Wakatsuki, Soichi},
abstractNote = {An integrated client-server control system (PCCS) with a unified relational database (PCDB) has been developed for high-throughput protein crystallography experiments on synchrotron beamlines. The major steps in protein crystallographic experiments (purification, crystallization, crystal harvesting, data collection, and data processing) are integrated into the software. All information necessary for performing protein crystallography experiments is stored in the PCDB database (except raw X-ray diffraction data, which is stored in the Network File Server). To allow all members of a protein crystallography group to participate in experiments, the system was developed as a multi-user system with secure network access based on TCP/IP secure UNIX sockets. Secure remote access to the system is possible from any operating system with X-terminal and SSH/X11 (Secure Shell with graphical user interface) support. Currently, the system covers the high-throughput X-ray data collection stages and is being commissioned at BL5A and NW12A (PF, PF-AR, KEK, Tsukuba, Japan)},
doi = {10.1063/1.2436451},
journal = {AIP Conference Proceedings},
number = 1,
volume = 879,
place = {United States},
year = {Fri Jan 19 00:00:00 EST 2007},
month = {Fri Jan 19 00:00:00 EST 2007}
}
  • An integrated controlling system and a unified database for high throughput protein crystallography experiments have been developed. Main features of protein crystallography experiments (purification, crystallization, crystal harvesting, data collection, data processing) were integrated into the software under development. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data that are stored in a central data server) in a MySQL relational database. The database contains four mutually linked hierarchical trees describing protein crystals, data collection of protein crystal and experimental data processing. A database editor was designed and developed. The editor supports basic database functions to view,more » create, modify and delete user records in the database. Two search engines were realized: direct search of necessary information in the database and object oriented search. The system is based on TCP/IP secure UNIX sockets with four predefined sending and receiving behaviors, which support communications between all connected servers and clients with remote control functions (creating and modifying data for experimental conditions, data acquisition, viewing experimental data, and performing data processing). Two secure login schemes were designed and developed: a direct method (using the developed Linux clients with secure connection) and an indirect method (using the secure SSL connection using secure X11 support from any operating system with X-terminal and SSH support). A part of the system has been implemented on a new MAD beam line, NW12, at the Photon Factory Advanced Ring for general user experiments.« less
  • No abstract prepared.
  • No abstract prepared.
  • RIKEN structural genomics beamlines, BL26B1 and B2 at the SPring-8, were constructed for the structural genomics research. The main feature of the beamline is full automation of the successive data collection to maximize the beamtime efficiency. The core part of the research and development is a newly developed sample management system composed of a sample auto-changer and a database system. BL26B1 has started the user operation, and commissioning of the automatic operation with the sample management system is being progressed at BL26B2.
  • A high-throughput Protein Crystallography beamline BL13B1 was constructed on a high-field (3.2 T) superconducting magnet, multi-pole (28 effective poles) wiggler (SW6) fan of the NSRRC storage ring. This field increase the critical energy from 2.14 keV for a 1.25 T normal conducting magnet to 4.82 keV. The 28 poles device, of period 60 mm, is capable to provide an intense X-ray beam up to 19 keV that allows a hard x-ray program to be developed on the relatively low energy National Synchrotron Radiation Research Center (NSRRC) ring (1.5 GeV). BL13B1 operates over the energy range from 6.5 keV to 19more » keV (1.92 angstrom to 0.65 angstrom). Optimized for MAD experiments, it is also suitable for monochromatic crystallography. The principal components of the beamline include a front end, vertically collimating premirror, double-crystal silicon (111) monochromator with a fixed-height exit beam, and a toroidal focusing mirror. The end station is equipped with a state-of-the-art ADSC Quantum315 CCD area detector, a high precision single-phi axis goniometer, a sample cooling system ({approx}100 K), a robotic sample changer for automatically sample mounting and centering, user-friendly data acquisition software (BLU-ICE), and powerful data processing software (HKL2000). The design and performance characteristics of this beamline will be described.« less