Protein crystallography for non‐crystallographers, or how to get the best (but not more) from published macromolecular structures

The number of macromolecular structures deposited in the Protein Data Bank now exceeds 45 000, with the vast majority determined using crystallographic methods. Thousands of studies describing such structures have been published in the scientific literature, and 14 Nobel prizes in chemistry or medicine have been awarded to protein crystallographers. As important as these structures are for understanding the processes that take place in living organisms and also for practical applications such as drug design, many non‐crystallographers still have problems with critical evaluation of the structural literature data. This review attempts to provide a brief outline of technical aspects of crystallography and to explain the meaning of some parameters that should be evaluated by users of macromolecular structures in order to interpret, but not over‐interpret, the information present in the coordinate files and in their description. A discussion of the extent of the information that can be gleaned from the coordinates of structures solved at different resolution, as well as problems and pitfalls encountered in structure determination and interpretation are also covered.

[1]  G. Phillips,et al.  Structural basis for catalysis by onconase. , 2008, Journal of molecular biology.

[2]  Stu Borman,et al.  PROBING LARGE PROTEIN SYSTEMS: STRUCTURE: Approach yields first detailed analysis of 456 protein nuclear pore complex , 2007 .

[3]  Zbigniew Dauter,et al.  Triclinic lysozyme at 0.65 A resolution. , 2007, Acta crystallographica. Section D, Biological crystallography.

[4]  Eric N Brown,et al.  Quality of protein crystal structures. , 2007, Acta crystallographica. Section D, Biological crystallography.

[5]  Gerard J Kleywegt,et al.  Separating model optimization and model validation in statistical cross-validation as applied to crystallography. , 2007, Acta crystallographica. Section D, Biological crystallography.

[6]  S. Borman STRUCTURE QUALITY: SCIENTIFIC PUBLISHING: Crystal structures in 'hotter'journals tend to have more errors , 2007 .

[7]  Randy J. Read,et al.  Crystallography: Crystallographic evidence for deviating C3b structure , 2007, Nature.

[8]  Zbigniew Dauter,et al.  Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them? , 2007, Acta crystallographica. Section D, Biological crystallography.

[9]  Michael Levitt,et al.  Growth of novel protein structural data , 2007, Proceedings of the National Academy of Sciences.

[10]  R. Ravelli,et al.  Radiation damage in macromolecular cryocrystallography. , 2006, Current opinion in structural biology.

[11]  R. Dawson,et al.  Structure of a bacterial multidrug ABC transporter , 2006, Nature.

[12]  M. Harding,et al.  Small revisions to predicted distances around metal sites in proteins. , 2006, Acta crystallographica. Section D, Biological crystallography.

[13]  Jay Painter,et al.  Electronic Reprint Biological Crystallography Optimal Description of a Protein Structure in Terms of Multiple Groups Undergoing Tls Motion Biological Crystallography Optimal Description of a Protein Structure in Terms of Multiple Groups Undergoing Tls Motion , 2005 .

[14]  Z. Dauter,et al.  Structure of DraD invasin from uropathogenic Escherichia coli: a dimer with swapped beta-tails. , 2006, Acta crystallographica. Section D, Biological crystallography.

[15]  I. Tanaka,et al.  Recent results on hydrogen and hydration in biology studied by neutron macromolecular crystallography , 2006, Cellular and Molecular Life Sciences CMLS.

[16]  A. Wlodawer,et al.  Atomic-resolution crystal structure of the proteolytic domain of Archaeoglobus fulgidus lon reveals the conformational variability in the active sites of lon proteases. , 2005, Journal of molecular biology.

[17]  S. Eom,et al.  The Active Site of a Lon Protease from Methanococcus jannaschii Distinctly Differs from the Canonical Catalytic Dyad of Lon Proteases* , 2004, Journal of Biological Chemistry.

[18]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[19]  Ying Zhang,et al.  Crystal structure of a novel antifungal protein distinct with five disulfide bridges from Eucommia ulmoides Oliver at an atomic resolution. , 2004, Journal of structural biology.

[20]  David C. Richardson,et al.  MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes , 2004, Nucleic Acids Res..

[21]  R E Cachau,et al.  Ultrahigh resolution drug design I: Details of interactions in human aldose reductase–inhibitor complex at 0.66 Å , 2004, Proteins.

[22]  A. Wlodawer,et al.  The Catalytic Domain of Escherichia coli Lon Protease Has a Unique Fold and a Ser-Lys Dyad in the Active Site* , 2004, Journal of Biological Chemistry.

[23]  Tom Alber,et al.  Automated protein crystal structure determination using ELVES. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Elspeth Garman,et al.  'Cool' crystals: macromolecular cryocrystallography and radiation damage. , 2003, Current opinion in structural biology.

[25]  Gérard Bricogne,et al.  Sheldrick's 1.2 A rule and beyond. , 2003, Acta crystallographica. Section D, Biological crystallography.

[26]  A. Wlodawer,et al.  Atomic resolution structure of Erwinia chrysanthemi L-asparaginase. , 2002, Acta crystallographica. Section D, Biological crystallography.

[27]  David Blow,et al.  Outline of Crystallography for Biologists , 2002 .

[28]  F. Allen The Cambridge Structural Database: a quarter of a million crystal structures and rising. , 2002, Acta crystallographica. Section B, Structural science.

[29]  Marjorie M. Harding,et al.  Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium. , 2002, Acta crystallographica. Section D, Biological crystallography.

[30]  A. Wlodawer,et al.  Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase. , 2001, Biochemistry.

[31]  C. B. Roth,et al.  Structure of MsbA from E. coli: a homolog of the multidrug resistance ATP binding cassette (ABC) transporters. , 2001, Science.

[32]  Bernhard Rupp,et al.  Questions about the structure of the botulinum neurotoxin B light chain in complex with a target peptide , 2001, Nature Structural Biology.

[33]  J Otlewski,et al.  Ultrahigh-resolution structure of a BPTI mutant. , 2001, Acta crystallographica. Section D, Biological crystallography.

[34]  Raymond C. Stevens,et al.  Structural Basis for BABIM Inhibition of Botulinum Neurotoxin Type B Protease , 2000 .

[35]  C. Vonrhein,et al.  Structure of the 30S ribosomal subunit , 2000, Nature.

[36]  F. Schluenzen,et al.  Structure of Functionally Activated Small Ribosomal Subunit at 3.3 Å Resolution , 2000, Cell.

[37]  T. Steitz,et al.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. , 2000, Science.

[38]  S. Andrews,et al.  Substrate Specificity in Glycoside Hydrolase Family 10 , 2000, The Journal of Biological Chemistry.

[39]  V Lamzin,et al.  Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Poul Nissen,et al.  Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit , 1999, Nature.

[41]  M. Harding,et al.  The geometry of metal-ligand interactions relevant to proteins. , 1999, Acta crystallographica. Section D, Biological crystallography.

[42]  D. Stuart,et al.  The atomic structure of the bluetongue virus core , 1998, Nature.

[43]  V. Mikol,et al.  Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its metal cofactor: high level of similarity of the active site with other viral integrases. , 1998, Journal of molecular biology.

[44]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[45]  D. Davies,et al.  Three new structures of the core domain of HIV-1 integrase: an active site that binds magnesium. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Chris Sander,et al.  Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network. , 1998, Journal of molecular biology.

[47]  P. Andrew Karplus,et al.  Improved R-factors for diffraction data analysis in macromolecular crystallography , 1997, Nature Structural Biology.

[48]  M. Weiss,et al.  On the use of the merging R factor as a quality indicator for X-ray data , 1997 .

[49]  M. Jaskólski,et al.  High-resolution structure of the catalytic domain of avian sarcoma virus integrase. , 1995, Journal of molecular biology.

[50]  R A Sayle,et al.  RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.

[51]  G J Kleywegt,et al.  Where freedom is given, liberties are taken. , 1995, Structure.

[52]  A. Engelman,et al.  Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. , 1994, Science.

[53]  A. Danchin,et al.  The catalytic domain of Escherichia coli K-12 adenylate cyclase as revealed by deletion analysis of the cya gene , 1994, Molecular and General Genetics MGG.

[54]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[55]  I. D. Brown,et al.  Chemical and Steric Constraints in Inorganic Solids , 1992 .

[56]  A. Brunger Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. , 1992 .

[57]  R. Huber,et al.  Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement , 1991 .

[58]  Michael O'Keeffe,et al.  Bond-valence parameters for solids , 1991 .

[59]  G. Sheldrick Phase annealing in SHELX-90: direct methods for larger structures , 1990 .

[60]  T. Jones,et al.  Between objectivity and subjectivity , 1990, Nature.

[61]  M. Jaskólski,et al.  Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. , 1989, Science.

[62]  I. Andersson,et al.  Reexamination of the Three-Dimensional Structure of the Small Subunit of RuBisCo from Higher Plants , 1989, Science.

[63]  M. Navia,et al.  Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1 , 1989, Nature.

[64]  Maria Miller,et al.  Crystal structure of a retroviral protease proves relationship to aspartic protease family , 1989, Nature.

[65]  M S Chapman,et al.  Tertiary structure of plant RuBisCO: domains and their contacts. , 1988, Science.

[66]  W. Hendrickson,et al.  True identity of a diffraction pattern attributed to valyl tRNA , 1983, Nature.

[67]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[68]  B. Matthews Solvent content of protein crystals. , 1968, Journal of molecular biology.

[69]  C. Singh Location of hydrogen atoms in certain heterocyclic compounds , 1965 .

[70]  G. N. Ramachandran,et al.  Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units. , 1965, Biophysical journal.

[71]  J. Kendrew,et al.  A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis , 1958, Nature.

[72]  Robert Huber,et al.  Structure quality and target parameters , 2006 .

[73]  A. A. Milne,et al.  クマのプーさん = Winnie‐the‐Pooh , 2006 .

[74]  Erik Smitterberg,et al.  Tests for statistical significance , 2005 .

[75]  Margaret H. Butler,et al.  Three-Dimensional Structure of I to , 2004 .

[76]  George M Sheldrick,et al.  Is the bond-valence method able to identify metal atoms in protein structures? , 2003, Acta crystallographica. Section D, Biological crystallography.

[77]  W. Delano The PyMOL Molecular Graphics System , 2002 .

[78]  T. Hahn International tables for crystallography , 2002 .

[79]  F. Schluenzen,et al.  Structure of Functionally Activated Small Ribosomal Subunit , 2000 .

[80]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[81]  M. Jaskólski,et al.  The catalytic domain of avian sarcoma virus integrase: conformation of the active-site residues in the presence of divalent cations. , 1996, Structure.

[82]  J. Drenth Principles of protein x-ray crystallography , 1994 .

[83]  G. Rhodes Crystallography Made Crystal Clear , 1993 .

[84]  A. Brünger Free R value: a novel statistical quantity for assessing the accuracy of crystal structures , 1992, Nature.

[85]  W. Hendrickson Stereochemically restrained refinement of macromolecular structures. , 1985, Methods in enzymology.

[86]  A. Wlodawer,et al.  Neutron diffraction of crystalline proteins. , 1982, Progress in biophysics and molecular biology.

[87]  D. Sherry The bond. , 1979, Nursing.

[88]  G. D. Rieck,et al.  International tables for X-ray crystallography , 1962 .