Literature DB >> 24034303

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination.

Alexander Wlodawer1, Wladek Minor, Zbigniew Dauter, Mariusz Jaskolski.   

Abstract

The number of macromolecular structures deposited in the Protein Data Bank now approaches 100,000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation.
© 2013 FEBS.

Entities:  

Keywords:  data collection and processing; electron density maps; protein crystallography; structure quality; structure refinement; structure solution; structure validation

Mesh:

Substances:

Year:  2013        PMID: 24034303      PMCID: PMC4080831          DOI: 10.1111/febs.12495

Source DB:  PubMed          Journal:  FEBS J        ISSN: 1742-464X            Impact factor:   5.542


  112 in total

1.  The Protein Data Bank.

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Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

Review 2.  Validation of protein crystal structures.

Authors:  G J Kleywegt
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-03

3.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.

Authors:  N Ban; P Nissen; J Hansen; P B Moore; T A Steitz
Journal:  Science       Date:  2000-08-11       Impact factor: 47.728

4.  Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution.

Authors:  F Schluenzen; A Tocilj; R Zarivach; J Harms; M Gluehmann; D Janell; A Bashan; H Bartels; I Agmon; F Franceschi; A Yonath
Journal:  Cell       Date:  2000-09-01       Impact factor: 41.582

5.  Can anomalous signal of sulfur become a tool for solving protein crystal structures?

Authors:  Z Dauter; M Dauter; E de La Fortelle; G Bricogne; G M Sheldrick
Journal:  J Mol Biol       Date:  1999-05-28       Impact factor: 5.469

6.  Automated protein model building combined with iterative structure refinement.

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Journal:  Nat Struct Biol       Date:  1999-05

7.  High-resolution structure of bovine pancreatic trypsin inhibitor with altered binding loop sequence.

Authors:  H Czapinska; J Otlewski; S Krzywda; G M Sheldrick; M Jaskólski
Journal:  J Mol Biol       Date:  2000-02-04       Impact factor: 5.469

8.  Applications of synchrotron radiation to protein crystallography: preliminary results.

Authors:  J C Phillips; A Wlodawer; M M Yevitz; K O Hodgson
Journal:  Proc Natl Acad Sci U S A       Date:  1976-01       Impact factor: 11.205

9.  Crystallization of nerve growth factor from mouse submaxillary glands.

Authors:  A Wlodawer; K O Hodgson; E M Shooter
Journal:  Proc Natl Acad Sci U S A       Date:  1975-03       Impact factor: 11.205

10.  Novel approach to phasing proteins: derivatization by short cryo-soaking with halides.

Authors:  Z Dauter; M Dauter; K R Rajashankar
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-02
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  35 in total

1.  Progress in protein crystallography.

Authors:  Zbigniew Dauter; Alexander Wlodawer
Journal:  Protein Pept Lett       Date:  2016       Impact factor: 1.890

2.  On the reliability of peptide nonplanarity seen in ultra-high resolution crystal structures.

Authors:  Andrew E Brereton; P Andrew Karplus
Journal:  Protein Sci       Date:  2016-02-08       Impact factor: 6.725

3.  Charge-density analysis of an iron-sulfur protein at an ultra-high resolution of 0.48 Å.

Authors:  Yu Hirano; Kazuki Takeda; Kunio Miki
Journal:  Nature       Date:  2016-05-18       Impact factor: 49.962

Review 4.  X-ray crystallography over the past decade for novel drug discovery - where are we heading next?

Authors:  Heping Zheng; Katarzyna B Handing; Matthew D Zimmerman; Ivan G Shabalin; Steven C Almo; Wladek Minor
Journal:  Expert Opin Drug Discov       Date:  2015-07-15       Impact factor: 6.098

Review 5.  The sweet spot: defining virus-sialic acid interactions.

Authors:  Jennifer E Stencel-Baerenwald; Kerstin Reiss; Dirk M Reiter; Thilo Stehle; Terence S Dermody
Journal:  Nat Rev Microbiol       Date:  2014-09-29       Impact factor: 60.633

Review 6.  A close look onto structural models and primary ligands of metallo-β-lactamases.

Authors:  Joanna E Raczynska; Ivan G Shabalin; Wladek Minor; Alexander Wlodawer; Mariusz Jaskolski
Journal:  Drug Resist Updat       Date:  2018-08-25       Impact factor: 18.500

7.  Revealing the architecture of protein complexes by an orthogonal approach combining HDXMS, CXMS, and disulfide trapping.

Authors:  Kunhong Xiao; Yang Zhao; Minjung Choi; Hongda Liu; Adi Blanc; Jiang Qian; Thomas J Cahill; Xue Li; Yunfang Xiao; Lisa J Clark; Sheng Li
Journal:  Nat Protoc       Date:  2018-05-24       Impact factor: 13.491

8.  A comparative cross-linking strategy to probe conformational changes in protein complexes.

Authors:  Carla Schmidt; Carol V Robinson
Journal:  Nat Protoc       Date:  2014-08-21       Impact factor: 13.491

Review 9.  αKlotho-FGF23 interactions and their role in kidney disease: a molecular insight.

Authors:  Edward R Smith; Stephen G Holt; Tim D Hewitson
Journal:  Cell Mol Life Sci       Date:  2019-07-26       Impact factor: 9.261

10.  Resolving the cofactor-binding site in the proline biosynthetic enzyme human pyrroline-5-carboxylate reductase 1.

Authors:  Emily M Christensen; Sagar M Patel; David A Korasick; Ashley C Campbell; Kurt L Krause; Donald F Becker; John J Tanner
Journal:  J Biol Chem       Date:  2017-03-03       Impact factor: 5.157

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