Literature DB >> 11937051

Homo crystallographicus--quo vadis?

Gerard J Kleywegt1, T Alwyn Jones.   

Abstract

As macromolecular crystal structures are determined and refined in an increasingly automated fashion, careful assessment of the reliability and quality of the resulting models becomes increasingly important. Here, we analyze various issues related to the reliability and quality of macromolecular crystal structures deposited between 1991 and 2000. We find that the average resolution at which these structures are determined is essentially constant. In line with this observation, the average quality as measured by Ramachandran analysis does not improve as a function of time. On the other hand, an observed decrease of the average discrepancy between free and conventional R values suggests that the fit of model and data is improving. Finally, we present a surprising correlation between the tendency of crystallographers to deposit their experimental data and the free R values of their models.

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Year:  2002        PMID: 11937051     DOI: 10.1016/s0969-2126(02)00743-8

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  21 in total

1.  A use of Ramachandran potentials in protein solution structure determinations.

Authors:  Ivano Bertini; Gabriele Cavallaro; Claudio Luchinat; Irene Poli
Journal:  J Biomol NMR       Date:  2003-08       Impact factor: 2.835

2.  Definition of a new information-based per-residue quality parameter.

Authors:  Sander B Nabuurs; Elmar Krieger; Chris A E M Spronk; Aart J Nederveen; Gert Vriend; Geerten W Vuister
Journal:  J Biomol NMR       Date:  2005-10       Impact factor: 2.835

3.  Estimating the accuracy of protein structures using residual dipolar couplings.

Authors:  Katya Simon; Jun Xu; Chinpal Kim; Nikolai R Skrynnikov
Journal:  J Biomol NMR       Date:  2005-10       Impact factor: 2.835

4.  Structure and function of a potent agonist for the semi-invariant natural killer T cell receptor.

Authors:  Dirk M Zajonc; Carlos Cantu; Jochen Mattner; Dapeng Zhou; Paul B Savage; Albert Bendelac; Ian A Wilson; Luc Teyton
Journal:  Nat Immunol       Date:  2005-07-10       Impact factor: 25.606

5.  Structural Basis of the Oncogenic Interaction of Phosphatase PRL-1 with the Magnesium Transporter CNNM2.

Authors:  Paula Giménez-Mascarell; Iker Oyenarte; Serge Hardy; Tilman Breiderhoff; Marchel Stuiver; Elie Kostantin; Tammo Diercks; Angel L Pey; June Ereño-Orbea; María Luz Martínez-Chantar; Reham Khalaf-Nazzal; Felix Claverie-Martin; Dominik Müller; Michel L Tremblay; Luis Alfonso Martínez-Cruz
Journal:  J Biol Chem       Date:  2016-11-29       Impact factor: 5.157

6.  Structural basis for the retroreduction of inactivated peroxiredoxins by human sulfiredoxin.

Authors:  Thomas J Jönsson; Michael S Murray; Lynnette C Johnson; Leslie B Poole; W Todd Lowther
Journal:  Biochemistry       Date:  2005-06-21       Impact factor: 3.162

7.  The Phenix software for automated determination of macromolecular structures.

Authors:  Paul D Adams; Pavel V Afonine; Gábor Bunkóczi; Vincent B Chen; Nathaniel Echols; Jeffrey J Headd; Li-Wei Hung; Swati Jain; Gary J Kapral; Ralf W Grosse Kunstleve; Airlie J McCoy; Nigel W Moriarty; Robert D Oeffner; Randy J Read; David C Richardson; Jane S Richardson; Thomas C Terwilliger; Peter H Zwart
Journal:  Methods       Date:  2011-07-29       Impact factor: 3.608

8.  The compatible-solute-binding protein OpuAC from Bacillus subtilis: ligand binding, site-directed mutagenesis, and crystallographic studies.

Authors:  Sander H J Smits; Marina Höing; Justin Lecher; Mohamed Jebbar; Lutz Schmitt; Erhard Bremer
Journal:  J Bacteriol       Date:  2008-06-20       Impact factor: 3.490

9.  Structure of Alzheimer's disease amyloid precursor protein copper-binding domain at atomic resolution.

Authors:  Geoffrey Kwai-Wai Kong; Julian J Adams; Roberto Cappai; Michael W Parker
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2007-09-19

10.  Re-refinement from deposited X-ray data can deliver improved models for most PDB entries.

Authors:  Robbie P Joosten; Thomas Womack; Gert Vriend; Gérard Bricogne
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
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