skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Robust indexing for automatic data collection

Journal Article · · Journal of Applied Crystallography
 [1];  [1];  [1]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Dept. of Physical Biosciences

Improved methods for indexing diffraction patterns from macromolecular crystals are presented. The novel procedures include a more robust way to verify the position of the incident X-ray beam on the detector, an algorithm to verify that the deduced lattice basis is consistent with the observations, and an alternative approach to identify the metric symmetry of the lattice. These methods help to correct failures commonly experienced during indexing, and increase the overall success rate of the process. Rapid indexing, without the need for visual inspection, will play an important role as beamlines at synchrotron sources prepare for high-throughput automation.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1625642
Journal Information:
Journal of Applied Crystallography, Vol. 37, Issue 3; ISSN 0021-8898
Publisher:
International Union of CrystallographyCopyright Statement
Country of Publication:
United States
Language:
English

Cited By (44)

Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control system journal November 2014
Data systems for the Linac coherent light source journal January 2017
Structure of photosystem II and substrate binding at room temperature journal November 2016
Methods development for diffraction and spectroscopy studies of metalloenzymes at X-ray free-electron lasers journal July 2014
New Python-based methods for data processing journal June 2013
Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers journal March 2014
The complex of ferric-enterobactin with its transporter from Pseudomonas aeruginosa suggests a two-site model journal August 2019
Cellular and viral peptides bind multiple sites on the N-terminal domain of clathrin text January 2017
Autoindexing diffraction images with iMosflm journal June 2013
Pathological macromolecular crystallographic data affected by twinning, partial-disorder and exhibiting multiple lattices for testing of data processing and refinement tools journal October 2018
Human Rotavirus VP6-Specific Antibodies Mediate Intracellular Neutralization by Binding to a Quaternary Structure in the Transcriptional Pore journal May 2013
WrpA Is an Atypical Flavodoxin Family Protein under Regulatory Control of the Brucella abortus General Stress Response System journal February 2016
TssA from Burkholderia cenocepacia : expression, purification, crystallization and crystallographic analysis journal August 2018
SPIND : a reference-based auto-indexing algorithm for sparse serial crystallography data journal January 2019
Indexing grazing-incidence X-ray diffraction patterns of thin films: lattices of higher symmetry journal April 2019
Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers journal February 2017
Mechanism of DNA loading by the DNA repair helicase XPD journal February 2016
Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature journal February 2013
Preacinetobactin not acinetobactin is essential for iron uptake by the BauA transporter of the pathogen Acinetobacter baumannii journal December 2018
Radiation damage in room-temperature data acquisition with the PILATUS 6M pixel detector journal April 2011
Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy journal July 2014
Best practices for high data-rate macromolecular crystallography (HDRMX) journal January 2020
S -Adenosyl- S -carboxymethyl- L -homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA journal May 2013
Fully automatic characterization and data collection from crystals of biological macromolecules journal July 2015
Cellular and viral peptides bind multiple sites on the N-terminal domain of clathrin: MUENZNER journal December 2016
Structural insights into the function of type VI secretion system TssA subunits journal November 2018
A structural model for microtubule minus-end recognition and protection by CAMSAP proteins journal October 2017
Decision making in xia 2 journal June 2013
Data processing and analysis with the autoPROC toolbox journal March 2011
TonB-Dependent Receptor Repertoire of Pseudomonas aeruginosa for Uptake of Siderophore-Drug Conjugates journal March 2018
Human immunoglobulin E flexes between acutely bent and extended conformations journal March 2014
Anti-citrullinated protein antibodies cause arthritis by cross-reactivity to joint cartilage journal July 2017
Structural Insights into the Mechanism and Inhibition of the β-Hydroxydecanoyl-Acyl Carrier Protein Dehydratase from Pseudomonas aeruginosa journal January 2013
Structural Mechanism for Modulation of Synaptic Neuroligin-Neurexin Signaling by MDGA Proteins journal September 2017
Diffuse X-Ray Scattering to Model Protein Motions journal February 2014
Automation and Experience of Controlled Crystal Dehydration: Results from the European Synchrotron HC1 Collaboration journal January 2015
RGM co-receptors add complexity to BMP signaling journal June 2015
Long lasting neutralization of C5 by SKY59, a novel recycling antibody, is a potential therapy for complement-mediated diseases journal April 2017
Crystal structure of the human Tip41 orthologue, TIPRL, reveals a novel fold and a binding site for the PP2Ac C-terminus journal August 2016
X-ray data processing journal October 2017
Goniometer-based femtosecond X-ray diffraction of mutant 30S ribosomal subunit crystals journal April 2015
Implications for Collagen Binding from the Crystallographic Structure of Fibronectin 6FnI1–2FnII7FnI journal October 2010
The Salmonella Effector SpvD Is a Cysteine Hydrolase with a Serovar-specific Polymorphism Influencing Catalytic Activity, Suppression of Immune Responses, and Bacterial Virulence journal December 2016
Automatic Fortran to C++ conversion with FABLE journal May 2012

Similar Records

Robust indexing for automatic data collection
Journal Article · Tue Dec 09 00:00:00 EST 2003 · Journal of Applied Crystallography · OSTI ID:1625642

Lawrence Berkeley Lab Indexing Toolbox
Software · Mon Sep 08 00:00:00 EDT 2003 · OSTI ID:1625642

SU-C-9A-02: Structured Noise Index as An Automated Quality Control for Nuclear Medicine: A Two Year Experience
Journal Article · Sun Jun 01 00:00:00 EDT 2014 · Medical Physics · OSTI ID:1625642