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

Title: Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry

Journal Article · · Acta Crystallographica. Section D. Structural Biology
 [1]
  1. Univ. of Oklahoma, Oklahoma City, OK (United States). Health Sciences Center, Dept. of Biochemistry and Molecular Biology
+ Show Author Affiliations

Using direct methods starting from random phases, the crystal structure of a 32-base-pair RNA (675 non-H RNA atoms in the asymmetric unit) was determined using only the native diffraction data (resolution limit 1.05 Å) and the computer programSIR2014. The almost three helical turns of the RNA in the asymmetric unit introduced partial or imperfect translational pseudosymmetry (TPS) that modulated the intensities when averaged by thelMiller indices but still escaped automated detection. Almost six times as many random phase sets had to be tested on average to reach a correct structure compared with a similar-sized RNA hairpin (27 nucleotides, 580 non-H RNA atoms) without TPS. Lastly, more sensitive methods are needed for the automated detection of partial TPS.

Research Organization:
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)
Sponsoring Organization:
USDOE; National Institutes of Health (NIH)
Grant/Contract Number:
P20 GM103640
OSTI ID:
1344902
Journal Information:
Acta Crystallographica. Section D. Structural Biology, Vol. 72, Issue 4; ISSN 2059-7983
Publisher:
IUCrCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 5 works
Citation information provided by
Web of Science

References (49)

PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM journal March 2011
The Protein Data Bank journal January 2000
Direkte Methoden für Strukturen mit Überstruktureffekten journal May 1982
Crystal structure determination and refinement via SIR2014 journal January 2015
The revenge of the Patterson methods. I. Protein ab initio phasing journal July 2006
Solving crystal structures in P 1: an automated procedure for finding an allowed origin in the correct space group journal April 2000
A robust tangent procedure journal October 2013
Ab initio phasing of proteins with heavy atoms at non-atomic resolution: pushing the size limit of solvable structures up to 7890 non-H atoms in the asymmetric unit journal April 2008
Advances in the free lunch method journal September 2007
Direct methods and superstructures. I. Effects of the pseudotranslations on the reciprocal space journal November 1985
Direct methods and structures showing superstructure effects.II. A probabilistic theory of triplet invariants journal January 1987
Direct methods and structures showing superstructure effects. III. A general mathematical model journal March 1988
Direct methods and structures showing superstructure effects. IV. A new approach for phase solution journal March 1988
MolProbity : all-atom structure validation for macromolecular crystallography journal December 2009
Pathological crystallography: case studies of several unusual macromolecular crystals journal June 2005
ACORN 2: new developments of the ACORN concept journal August 2009
X-ray crystallographic analysis of the hydration of A- and B-form DNA at atomic resolution journal January 1998
Features and development of Coot journal March 2010
Scaling and assessment of data quality journal December 2005
The program SAPI and its applications. II. The combination of Patterson superposition and direct methods journal September 1988
The program SAPI and its applications. I. Automatic search of pseudo-systematic extinction for solving superstructures journal September 1988
The influence of rational dependence on the probability distribution of structure factors journal September 1984
Direct-methods determination of an RNA/DNA hybrid decamer at 1.15 Å resolution journal February 2001
Rational dependence and the renormalization of structure factors for phase determination journal November 1959
On the application of direct methods to oligonucleotide crystallography journal November 1994
Patterson-guided ab initio analysis of structures with helical symmetry journal September 2008
Online_DPI : a web server to calculate the diffraction precision index for a protein structure journal April 2015
Relaxation of the resolution requirements for direct-methods phasing journal May 2011
Mean phase error and the map-correlation coefficient journal November 1993
Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution journal June 2014
A statistical treatment of superlattice reflexions journal February 1953
Shake-and-Bake on the grid journal September 2007
Use of an ion-binding site to bypass the 1000-atom limit to structure determination by direct methods journal September 2004
Extension to 2268 atoms of direct methods in the ab initio determination of the unknown structure of bacteriophage P22 lysozyme journal January 2006
The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate journal August 2011
electronic Ligand Builder and Optimization Workbench ( eLBOW ): a tool for ligand coordinate and restraint generation journal September 2009
Sheldrick's 1.2 Å rule and beyond journal February 2003
Systematic Detection of Internal Symmetry in Proteins Using CE-Symm journal May 2014
A fast selenium derivatization strategy for crystallization and phasing of RNA structures journal February 2009
Charge Flipping at Work:  A Case of Pseudosymmetry journal July 2006
New parameters for the refinement of nucleic acid-containing structures journal January 1996
Intensity statistics in the presence of translational noncrystallographic symmetry journal January 2013
Structure of the Parallel Duplex of Poly(A) RNA: Evaluation of a 50 Year-Old Prediction journal June 2013
Phase annealing in SHELX-90: direct methods for larger structures journal June 1990
A short history of SHELX journal December 2007
Ab initio phasing of a 4189-atom protein structure at 1.2 Å resolution journal December 2000
Modern Applied Statistics with S book August 2002
Surprises and pitfalls arising from (pseudo)symmetry journal December 2007

Cited By (1)

The structure of denisovite, a fibrous nanocrystalline polytypic disordered `very complex' silicate, studied by a synergistic multi-disciplinary approach employing methods of electron crystallography and X-ray powder diffraction journal March 2017

Similar Records

ANS complex of St John’s wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning
Journal Article · Wed Apr 01 00:00:00 EDT 2015 · Acta Crystallographica. Section D: Biological Crystallography · OSTI ID:1344902
+3 more
Crystallization and X-ray diffraction analysis of the Trp/amber editing site of hepatitis delta virus (+)RNA: a case of rational design
Journal Article · Thu Dec 01 00:00:00 EST 2005 · Acta Crystallographica. Section F · OSTI ID:1344902
Translation of the edited mRNA for cytochrome b in trypanosome mitochondria
Journal Article · Tue Feb 01 00:00:00 EST 2000 · Science · OSTI ID:1344902

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
RNA structure determination
Patterson analysis
helical symmetry
ab initio phasing
noncrystallographic symmetry