Determination of macromolecular structures by X-ray crystallography

A selection of articles

Master degree in structural biology. University of Strasbourg

 

This is a my strongly biais selection  of articles for Master and PhD students in structural biology.  There are many others very good papers.

Molecular biology for structural studies

Symmetry and Space groups

Macromolecular crystallization

X-ray diffraction by a cristal

X-ray data collection

The solutions of the phase problem

Isomorphous replacement and  anomalous diffraction

Site-specific radiation damage

Molecular (Re)placement

Direct Methods

Electron density  maps

Model building and refinement

Structure validations

Macromolecular crystallography programs

3D database: PDB-RCSB

High-resolution X-ray structures

Structure Factors and algorythms

Links

Structural genomic initiatives

Mathematical techniques

To understand statistics

Back to basic Mathematics

Back to basic Physics

Other methods in structural biology

XFEL

    Celebrating a century of X-ray crystallography

• Crystallography at 100, SCIENCE VOL 343 7 MARCH 2014
• Patrick Cramer, "A Tale of Chromatin and Transcription in 100 Structures", Cell 159, November 20, 2014
• Yigong Shi1, "A Glimpse of Structural Biology through X-Ray Crystallography", Cell 159, November 20, 2014
  

A selection of crystallographic textbooks or reviews articles

• M Chruszcz, A Wlodawer, W Minor "Determination of Protein Structures—A Series of Fortunate Events"
• Biophysical Journal Volume 95 July 2008 1–9   [PDF]
• A Wlodawer, W Minor, Z Dauter and M Jaskolski "Protein crystallography for non-crystallographers...."
• FEBS Journal 2008 Jan;275(1):1-21.   [PDF]
• D L Minor, Jr "The Neurobiologist’s Guide to Structural Biology: A Primer on ..."
• Neuron 54, May 24, 2007 [PDF]
• A. Schmidt,V. S. Lamzin, "From atoms to proteins", 
• Cell. Mol. Life Sci. 64 (2007) 1959 – 1969.   [PDF]
• Dauter Z. (2006), "Current state and prospects of macromolecular crystallography." 
• Acta Cryst. D62, 1-11. [PDF]
• Acharya KR, Lloyd MD. "The advantages and limitations of protein crystal structures
• "Trends Pharmacol Sci. 2005 Jan;26(1):10-4. [PDF]
  

• "The optical principles of the Diffraction of X-rays", R.W. James, 1982, OX Bow Press.
• “Fourier Methods in Crystallography”, G.N. Ramachandran, R. Srinivasan, 1970, Wiley.
• "X-Ray Charge Densities and Chemical Bonding", P. Coppens, (1997), IUCr.
• "Dynamical Theory of X-Ray Diffraction", A. Authier, (2001), IUCr.
• "Elements of Modern X-ray Physics", Jens Als-Nielsen, Des McMorrow, (2011), 2nd Edition
• "Phasing in Crystallography: A Modern Perspective", C. Giacovazzo, (2013)
  

• Tables Internationales de cristallographie Volume F. "Crystallography of biological Macromolecules", (2012), Kluwer Academic Press.
• Tables Internationales de cristallographie Volume B. "Reciprocal Space", (2010), Kluwer Academic Press.
• B. Rupp,"Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology",  (2007)

• "Crystallography and complementary methods", Acta Cryst D71, January 2015
• "Data collection and processing", Acta Cryst, D69, July 2013
  
• "Model building, refinement and validation", Acta Cryst, D68, April 2012
• "From crystal to structure with CCP4, Acta Cryst, D67, April 2011
• "Experimental phasing and radiation damage", Acta Cryst, D66, April 2010
• "Low-resolution structure determination and validation", Acta Cryst, D65, February 2009
• "Molecular replacement", Acta Cryst D64, Vol.1 January 2008
• "Crystallography of complexes". Acta Cryst, D63, January 2007.
• "Data collection and analysis". Acta Cryst , D62, Janvier 2006.
• "Structural Proteomics in Europe". Acta Cryst , D62, Octobre 2006.
• "Model building and refinement". Acta Cryst D60, Vol.12, December 2004.
• "Experimental Phasing". Acta Cryst D59, Vol.11, November 2003.

• Phenix Computational Crystallography Newsletter

• D.S. Sivia, "Data Analysis : a Bayesian Tutorial", 1996, 2006, Oxford University Press.
• G. Cowan, "Statistical Data Analysis", 1998, Oxford University Press.
• Statistical Descriptors in Crystallography (IUCr)

• "Crystallography of complexes". Acta Cryst, D63, January 2007.
• "Structural Proteomics in Europe". Acta Cryst , D62, Octobre 2006.
• CW Chung, "The use of biophysical methods increases success in obtaining liganded crystal structures"
• Acta Cryst. (2007). D63, 62–71      [PDF]

Symmetry and Space groups

• Crystallographic Space Group Diagrams and Tables
• International table of  de cristallography Volume A. "Space-group symmetry", (1993), Kluwer Academic Press.
• Symmetry operators
• Space group decoder
• "Gallery of direct-space asymmetric units".
• "Explore symmetry"
• Display symmetry 
• Wikipédia, Cristallography

Macromolecular crystallization

• "Progress in Biophysics and Molecular Biology", (2005), Vol 88, issue 3. 
• "Structural Biology of Membrane Proteins", Methods, Volume 41, Issue 4, Pages 353-488 (April 2007).
• Chayen NE, Saridakis E. "Protein crystallization: from purified protein to diffraction-quality crystal"
• Nature Methods,  Vol 5, Feb 2008,  147-153.  [PDF]
• Mueller M., Jenni S., Ban N. "Strategies for crystallization and structure determination of very large macromolecular assemblies"
• Current Opinion in Structural Biology 2007, 17:572–579.  [PDF]
• Ailong Kea A., Doudna  J.A. "Crystallization of RNA and RNA–protein complexes"
• Methods 34 (2004) 408–414.   [PDF]
• Chayen NE. " Turning protein crystallisation from an art into a science" 
• Curr Opin Struct Biol. 2004 Oct;14(5):577-83 [PDF]
• C. E. Kundrot. "Which strategy for a protein crystallization project?" 
• CMLS, Cell. Mol. Life Sci. 61 (2004) 525–536   [PDF]
• Hassel et al., "Crystallization of protein–ligand complexes"
• Acta Cryst. (2007). D63, 72-79    [PDF]
• TR Dafforn, "So how do you know you have a macromolecular complex?" 
• Acta Cryst. (2007). D63, 17–25    [PDF]
• Berry et al., "SPINE high-throughput crystallization, crystal imaging and recognition techniques..."
• Acta Cryst. (2006). D62, 1137-1149   [PDF]
• Peat TS, Christopher JA, Newman J. "Tapping the Protein Data Bank for crystallization information."
• Acta Crystallogr D Biol Crystallogr. 2005 Dec;61(Pt 12):1662-9.[PDF]
• Weselak et al.," Robotics for Automated Crystal Formation and Analysis" 
• Methods in Enzymology, (2003) V368, 45-76   [PDF]

X-ray diffraction by a cristal

• "A Guided Tour in Fourier Space", F. Tuinstra, [PDF]
• X-ray and neutron diffraction (R. B. Neder & T. H. Proffen)
• "50 Years of X-ray Diffraction" (1912-1962,IUCr)
• "Atomic Structure Factor Calculation. B. Rupp"
• Learn more on Fourier transform
• Kevin Cowtan's Book of Fourier
• Wikipedia Fourier transform 
• a small animation (in french)
• "FFTW home page"
  

X-ray data collection

• overview

• EF Garman TR SchneiderR, "Macromolecular Cryocrystallography"
• J. Appl. Cryst. (1997). 30, 211-237     [PDF]
• "Data collection and analysis". Acta Cryst , D62, Janvier 2006.
• Garman EF, Owen RL., (2006), "Cryocooling and radiation damage in macromolecular crystallography."
• Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):32-47. [PDF]
• Newman J.(2006) "A review of techniques for maximizing diffraction from a protein crystal in stilla." 
• Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):27-31.  [PDF] 
• Heras B, Martin JL., (2005). "Post-crystallization treatments for improving diffraction quality of protein crystals", 
• Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1173-80. [PDF]
• Dauter Z. (2005), "Efficient use of synchrotron radiation for macromolecular diffraction data collection."
• Prog Biophys Mol Biol. Oct;89(2):153-72.[PDF]

• X-ray sources and detectors

• M Hart, "What Can I Have As a Source of X-ray Synchrotron Radiation? A Primer for Potential Users"
• Methods in Enzymology, (2003) V368, 239-254   [PDF]
• "Synchrotron X-ray and Proton Beams in Structural Biology", 
• Progress in Biophysics and Molecular Biology", (2005), Vol 89, issue 3. 
• D. Flot et al., "The care and nurture of undulator data sets"
• Acta Cryst. (2006). D62, 65–71   [PDF]
• T L-M. Sorensen et al., "New light for science: synchrotron radiation in structural medicine",
• Trends in Biotechnology (2006), Vol.24 No.11, 500-508   [PDF]
• BioSync: A Structural Biologist's Guide to Synchrotron Facilities

• AutoIndexing

• Otwinowski Z, Minor W, (2001), "Denzo and Scalepack", Int. Tables. Cryst. Vol.F, [PDF] 
• Steller, R. Bolotovsky and M. G. Rossmann, (1997), "An Algorithm for Automatic Indexing of Oscillation Images using Fourier Analysis",
•  J. Appl. Cryst. 30, 1036-1040. [PDF] 
• MG  Rossmann and CG van Beek, (1999), "Data processing" Acta Cryst. D55, 1631-1640  [PDF]
• Harold R. Powell, (1999), "The Rossmann Fourier autoindexing algorithm in MOSFLM" Acta Cryst.D55, 1690-1695.[PDF] 
• N.K. Sauter, R.W. Grosse-Kunstleve, P.D. Adams, (2004), "Robust indexing for automatic data collection", 
• J. Appl. Cryst. 37, 399-409. [PDF]

• Data processing

• Leslie AG., "The integration of macromolecular diffraction data". Acta Cryst. (2006), D62, 48-57.[PDF]
• Tables Internationales de cristallographie Volume F." Crystallography of biological Macromolecules", (2001), Kluwer Academic Press.
• Dauter Z., Wilson, K. “Monochromatic Data Collection.”, pp 177-196.
• “Data Processing”, pp 209-243. 5 Articles de M.G. Rossman, A.G. Leslie, W. Kabsch, Z. Otwinoski, W. Minor
• Dauter Z., “Data Collection strategies.”, Acta Cryst. (1999), D55, 1703-1716.  [PDF]
• Evans P., "Scaling and assessment of quality data", Acta Cryst. (2006), D62, 72-82.  [PDF]
• Leslie, A.G.W., "Integration of macromolecular diffraction data", Acta Cryst. (1999). D55, 1696-1702   [PDF]
• Rossmann M., "Processing Oscillation Diffraction Data for Very Large Unit Cells with an Automatic Convolution Technique and Profile Fitting", 
• J. Appl. Cryst. (1979). 12, 225-238   [PDF]
• Data reduction: Pointless, Aimless, Truncate

• "Crystal Twinning"
• CCP4 documentation
• IUCR documentation
• Twin-Refinment with SHELXL

• "X-ray Data Collection Course", Phil Jeffrey, Feb 2006
• Applications : Simulations of Protein Crystallographic diffraction images  

Reciprocal space in real time (200 oscillation images, 1° oscillation per frame (Format avi))

• MLFSOM: A Full Simulation of the Diffraction Experiment James M. Holton, University of California.

The solutions of the phase problem

overview

• Taylor G. "The phase problem".Acta Crystallogr D Biol Crystallogr. 2003 Nov;59(Pt 11):1881-90. [PDF]
• "Phasing in Crystallography: A Modern Perspective", C. Giacovazzo, (2013)

Isomorphous replacement and  anomalous diffraction. Sub-stucture detemination and refinement, phasing.

• Bricogne G., (1991), " A Maximum-Likelihood therory of Heavy-Atom Parameter Refinement in Isomorphous Replacement Method", Proc. Daresbury Study Weekend," pp. 60-68. SERC Daresbury Laboratory, Warrington, U.K.  [PDF]
• De La Fortelle E., Bricogne, G. (1997). "Maximum -Likelihood Heavy-Atom Parameter Refinement for Multiple Isomorphous replaccement and Multiwavelength Anomalours Diffraction Methods",  Methods in Enzymology, 276A, 472-494. C.W. Carter & R.M. Sweet, eds    [PDF]
• Bricogne et al., (2003), "Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0"
• Acta Cryst. (2003). D59, 2023-2030. [PDF]
• Blow DM. (2003), "How Bijvoet made the difference: the growing power of anomalous scattering." Methods Enzymol. 374:3-22. [PDF]
• Weeks et al. (2003),  "Automatic solution of heavy-atom substructures"  Methods Enzymol. 374:37-83. [PDF]
• Roach J. (2003), "The Bijvoet-Difference Fourier Synthesis", Methods Enzymol. 374:137-145. [PDF]
• Dauter Z. (2006), "Estimation of anomalous signal in diffraction data." Acta Crystallogr D Biol Crystallogr. Aug;62(Pt 8):867-76  [PDF]
• Matthews B.W., "Five retracted structure reports: Inverted or incorrect?", Protein Science (2007), 16:1013–1016.   [PDF]
• Wang J, Wlodawer A, Dauter  Z. (2007),  " What happens when the signs of anomalous differences or the handedness of substructure are inverted? " 
• Acta Crystallogr D Biol Crystallogr. D63:751-758. [PDF]
• M Schiltz, G Bricogne, (2008), "Exploiting the anisotropy of anomalous scattering boosts the phasing power of SAD and MAD experiments"
• Acta Cryst. (2008). D64, 711–729   [PDF]

Site-specific radiation damage

• Schiltz M, Bricogne G. (2007). "Modelling and refining site-specific radiation damage in SAD/MAD phasing." 
• J Synchrotron Radiat. 2007 Jan;14(Pt 1):34-42. [PDF]
• Borek D, Ginell SL, Cymborowski M, Minor W, Otwinowski Z. "The many faces of radiation-induced changes."
• J Synchrotron Radiat. 2007 Jan;14(Pt 1):24-33. [PDF]
• M. H. Nanao, R B.G. Ravelli. "Phasing Macromolecular Structures with UV-Induced Structural Changes"
• Structure 14, 791–800, April 2006.   [PDF]

• more papers :
• "Radiation-damage induced phasing"'

Molecular (Re)placement

• P. Evans, A. McCoy, "An introduction to molecular replacement", Acta Cryst. (2008). D64, 1-10  [PDF]
• G. J. Barton, "Sequence alignment for molecular replacement", Acta Cryst. (2008). D64, 25-32  [PD
• A. J. McCoy, "Phaser crystallographic software", J. Appl. Cryst. (2007). 40, 658–674  [PDF]
• A. J. McCoy,"Solving structures of protein complexes by molecular replacement with Phaser ". Acta Cryst. (2007). D63, 32–41  [PDF]
• A. J. McCoy, R. W. Grosse-Kunstleve, L. C. Storoni and R. J. Read., Likelihood-enhanced fast translation functions ,Acta Cryst. (2005). D61, 458-464.
• L. C. Storoni, A. J. McCoy and R. J. Read, Likelihood-enhanced fast rotation functions, Acta Cryst. (2004). D60, 432-438.
• building a serach model :
• Schwarzenbacher R, Godzik A, Grzechnik SK, Jaroszewski L., "The importance of alignment accuracy for molecular replacement." 
• Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1229-36. [PDF]
• Few ideas from predictions. Site Web CASP, Proceedings
• Nayeem A, Sitkoff D, Krystek S Jr.  "A comparative study of available software for high-accuracy homology modeling: from sequence alignments to structural models". 
• Protein Sci. 2006 Apr;15(4):808-24.
• Suhre K, Sanejouand YH. "On the potential of normal-mode analysis for solving difficult molecular-replacement problems". 
• Acta Crystallogr D Biol Crystallogr. 2004 Apr;60(Pt 4):796-9.
• Suhre K, Sanejouand YH. "ElNemo: a normal mode web server for protein movement analysis and thegeneration of templates for molecular replacement". 
• Nucleic Acids Res. 2004 Jul 1;32
• Bricogne, G. (1997). "The Bayesian Statistical Viewpoint on Structure Determination: Basic Concepts and Examples",
•   Methods in Enzymology, 276A, 361-423. C.W. Carter & R.M. Sweet, eds.

Direct Methods

• "Phasing in Crystallography: A Modern Perspective", C. Giacovazzo, (2013)
• George M. Sheldrick, "The future of direct methods",
• IUCr Computing School, Siena, August 2005, [PDF]
• H. Schenk. An Introduction to Direct Methods. [HTML]
• J. Karle, " Recovering Phase Information from Intensity Data",  Nobel Prize lecture  1985
• H.A. Hauptman, "Direct Methods and Anomalous Dispersion",  Nobel Prize lecture  1985

Electron density  maps

• WA. Hendrickson, S Sheriff (1987),  “General Density Function Corresponding to X-ray Diffraction with Anomalous Scattering Included”  
• Acta Cryst.  A43, 121-125    [PDF] 
• Randy Read, "Introduction to fitting, refinement and validation."  [HTML]
• Phil Evans, "Fitting, Refinement and Validation."  [HTML]
• Randy Read, "Model Phases: Probabilities and Biais"
• Methods in Enzymology, 277, 110-128    [PDF] 
• Effects of errors:  Some movies (James Holton, Berkeley)
  
• 
  

Model building and refinement

• "Model building and refinement". Acta Cryst D60, Vol.12, December 2004.
• "Experimental Phasing". Acta Cryst D59, Vol.11, November 2003.

• "An introduction to stereochemical restraints", P. Evans,
•  Acta Cryst. (2007). D63, 58–61. [PDF]
• "Atomic Displacement Parameter Nomenclature", Trueblood et al.,
•  Acta Cryst. (1996). A52, 770-781.[PDF]
• "Macromolecular TLS Refinement in REFMAC at Moderate Resolutions", MD  Winn, GN Murshudov, MZ Papiz 
• Methods Enzymol. 374:300-321. [PDF]
• "Optimal description of a protein structure in terms of multiple groups undergoing TLS motion",  J. Painter, E. A. Merritt
• Acta Cryst. (2006). D62, 439–450 [PDF]
• TLS motion
• "Refinement of Macromolecular Structures by the Maximum-Likelihood Method", GN Murshudov, A Vagin, EJ Dodson
• Acta Cryst. (1997). D53, 240-255
• "Improved Structure Refinement Through Maximum Likelihood", N.S. Pannu, R.J. Read 
• Acta Cryst. (1996). A52, 659-668
• Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT, E. Blanc et al.
• Acta Cryst. (2004). D60, 2210-2221
  

Structure validations

• AA Vaguine, J Richellea and S. J. Wodaka, Acta Cryst. (1999). D55, 191-205
• "SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model " 
• "Practical Model Validation" (G. Kleywegt)
• "Whatif checks"
• "Judging the Quality of Macromolecular models" G Rhodes
• Some servers :
• Biotech    JCSG      MolProbity

Macromolecular crystallography programs

 3D database: PDB-RCSB

• "An Information Portal to Biological Macromolecular Structures"
• PDB format in details
• IUPAC 1998
• "OCA search"
• "HM Berman, "The Protein Data Bank: a historical perspective", 
• Acta Cryst. (2008). A64, 88–95  [PDF]

XFEL

• John C.H. Spence. " X-ray lasers and crystallography". IUCrJ (2014). 1, 151–152
• Chapman H. N., Caleman C.and Timneanu N., "Diffraction before destruction", Phil. Trans. R. Soc. B 369:20130313.
  
• V. Marx, "Structural biology: 'seeing' crystals the XFEL way". Nature Methods 11,903–908, (2014)
• J C H Spence, U Weierstall, and H N Chapman. "X-ray lasers for structural and dynamic biology". Rep. Prog. Phys. 75 (2012)

High-resolution X-ray structures

• A Schmidt,VS Lamzin, "From atoms to proteins", 
• Cell. Mol. Life Sci. 64 (2007) 1959 – 1969.   [PDF]
• C Lecomte et al. "Ultra-high-resolution X-ray structure of proteins",
•  CMLS, Cell. Mol. Life Sci. 61 (2004) 774–782   [PDF]

Structure Factors and methods

• Read R., "Structure factor statistics: Wilson statistics, SIGMAA."
• Bricogne, G. (1993), Fourier Transforms in Crystallography : Theory, Algorithms and Applications. 
• Tables Internationale de cristallographie Volume B. "Reciprocal Space", (1993), Kluwer Academic Press.
• Bricogne, G. (1997). "The Bayesian Statistical Viewpoint on Structure Determination: Basic Concepts and Examples", 
•  Methods in Enzymology, 276A, 361-423. C.W. Carter & R.M. Sweet, eds.
• A. J. McCoy, (2004),  "Liking Likelihood", Acta Cryst. . D60, 2169-2183 [PDF]  
• RJ. Morris, G Bricogne, "Sheldrick's 1.2A rule and beyond", 
• Acta Cryst. (2003). D59, 615-617.    [PDF]
• Morris RJ, Blanc E, Bricogne G, (2004), On the interpretation and use of <|E|2>(d*) profiles. 
• Acta Crystallogr D Biol Crystallogr. Feb;60(Pt 2):227-40.[PDF]

Mathematical techniques

• "Basic Maths for Protein Crystallographers"
•  "CCP4 Roadmaps"
• "Computational Crystallography Toolbox"
• Service Web
• Coordinate systems, operators, and transformations., Coordonnées (K. Cowtan)
• Crystallographic Symmetry in Real and Reciprocal Space (K. Cowtan)

Links

• A selection of software used in protein crystallography

• Macromolecular Crystallography course MRC-LMB
• Cours de Jean Pierre Lauriat
• Chem M230D course (UCLA)
• Crystallographic Tutorials (UCLA)
• "IUCR Teaching Phamplets"
• "IUCR Educational Resources"

• Protein Structure Initiative
• "search PSI"
• A example :  JCSG

Back to basic Mathematics  (in French)

• "Promenades mathématiques" (in French)
• "Chronologie des mathématiques" (in French)
• "Dynamaths" (in french)
• " les nombres complexes"
• "Formulaire de Trigonométrie"
• "Séries de Fourier"