MX : macromolecular crystallography

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This is very much an ongoing project to gather some of the more significant, thought-provoking and interesting literature references associated with crystallographic methods and the theory behind them. Programs have become sufficiently advanced that you can solve structures while knowing relatively little theory. This little collection is intended as an antidote to that.

This list is incomplete. You know it, and in particular I know it, but assembling the edifice from scratch turns out to require quite a lot of effort. If you want certain papers included in the list please send them to me (a PubMed URL is often the most useful for me) - see the Contact link in the menu bar. Many of the citations are culled from PubMed but the actual format is somewhat variable. In cases where I can, links to the PubMed or IUCr pages are linked in. In a few cases I've detected PDFs on the web, but for copyright reasons I do not host any PDFs here. The order within each subject is arbitrary, but I tend to put older pivotal references at the top, and cluster related papers (by author or technique) together. Sometimes I put a little commentary text on the end of the reference, particularly for older work or for papers that I've found especially useful.

Crystallization

• Matthews BW "Solvent content of protein crystals." J Mol Biol. 1968 Apr 28;33(2):491-7.
  • Kantardjieff KA, Rupp B. "Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals." Protein Science. 2003, 12, 1865-1871.
• Carter Jr CW, Carter CW "Protein crystallization using incomplete factorial experiments" J. Biol. Chem. (1979). 254, 12219-12223. (the definitive early paper on factorial screen design)
• Jancarik J, Kim SH "Sparse matrix sampling: a screening method for crystallization of proteins" J. Appl. Cryst. (1991). 24, 409-411. (immortalized as Hampton Research's Crystal Screen)
• Santarsiero BD, Yegian DT, Lee CC, Spraggon G, Gu J, Scheibe D, Uber DC, Cornell EW, Nordmeyer RA, Kolbe WF, Jin J, Jones AL, Jaklevic JM, Schultz PG, Stevens RC "An approach to rapid protein crystallization using nanodroplets" J. Appl. Cryst. (2002). 35, 278-281
• Stura EA, Wilson IA "Applications of the streak seeding technique in protein crystallization." J. Cryst. Growth (1991). 110, 270-282.
  • Walter TS, Mancini EJ, Kadlec J, Graham SC, Assenberg R, Ren J, Sainsbury S, Owens RJ, Stuart DI, Grimes JM, Harlos K. "Semi-automated microseeding of nanolitre crystallization experiments." Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Jan 1;64(Pt 1):14-8.
  • D'Arcy A, Villard F, Marsh M. "An automated microseed matrix-screening method for protein crystallization." Acta Crystallogr D Biol Crystallogr. 2007 Apr;63(Pt 4):550-4.
  • Obmolova G, Malia TJ, Teplyakov A, Sweet R, Gilliland GL. "Promoting crystallization of antibody-antigen complexes via microseed matrix screening." Acta Cryst. (2010). D66, 927-933
• Derewenda ZS. "The use of recombinant methods and molecular engineering in protein crystallization." Methods. 2004 Nov;34(3):354-63.
  • Derewenda ZS. "Rational protein crystallization by mutational surface engineering." Structure. 2004 Apr;12(4):529-35.
  • Derewenda ZS, Vekilov PG. "Entropy and surface engineering in protein crystallization." Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):116-24.
  • Cooper DR, Boczek T, Grelewska K, Pinkowska M, Sikorska M, Zawadzki M, Derewenda Z. "Protein crystallization by surface entropy reduction: optimization of the SER strategy." Acta Crystallogr D Biol Crystallogr. 2007 May;63(Pt 5):636-45.
  • Cieslik M, Derewenda ZS. "The role of entropy and polarity in intermolecular contacts in protein crystals." Acta Crystallogr D Biol Crystallogr. 2009 May;65(Pt 5):500-9.
  • Derewenda ZS. "Application of protein engineering to enhance crystallizability and improve crystal properties." Acta Crystallogr D Biol Crystallogr. 2010 May;66(Pt 5):604-15.
• Goldschmidt L, Cooper DR, Derewenda ZS, Eisenberg D. "Toward rational protein crystallization: A Web server for the design of crystallizable protein variants." Protein Sci. 2007 Aug;16(8):1569-76. (server link).
• various structural genomics consortia. "Protein production and purification." Nature Methods. 2008, 5, 135-146.
• Bai Y, Auperin TC, Tong L. "The use of in situ proteolysis in the crystallization of murine CstF-77." Acta Cryst. F Struct Biol Cryst Commun. 2007 Feb 1;63(Pt 2):135-8.
Dong, A and a cast of thousands. "In situ proteolysis for protein crystallization and structure determination." Nat Methods. 2007 Dec;4(12):1019-21.
• Gao X, Bain K, Bonanno JB, Buchanan M, Henderson D, Lorimer D, Marsh C, Reynes JA, Sauder JM, Schwinn K, Thai C, Burley SK. "High-throughput limited proteolysis/mass spectrometry for protein domain elucidation." J Struct Funct Genomics. 2005;6(2-3):129-34.

Data Collection

• Leslie AG, Powell HR, Winter G, Svensson O, Spruce D, McSweeney S, Love D, Kinder S, Duke E, Nave C. "Automation of the collection and processing of X-ray diffraction data - a generic approach." Acta Crystallogr D. 2002, 58:1924-1928.
• Hope H "Cryocrystallography of Biological Macromolecules: a Generally Applicable Method." Acta Crystallogr B. 1988 Feb 1;44 ( Pt 1):22-6.
  • Hope H, Frolow F, von Böhlen K, Makowski I, Kratky C, Halfon Y, Danz H, Webster P, Bartels KS, Wittmann HG, et al. "Cryocrystallography of ribosomal particles." Acta Crystallogr B. 1989 Apr 1;45 ( Pt 2):190-9.
  • Hope H "Crystallography of biological macromolecules at ultra-low temperature." Annu Rev Biophys Biophys Chem. 1990;19:107-26.
  • Teng, TY "Mounting of Crystals for Macromolecular Crystallography in a Free-standing Thin Film " J. Appl. Cryst. (1990). 23, 387-391
  • Rogers DW "Cryocrystallography." Structure (1994) 2, 1135-1140
  • Garman EF, Mitchell EP "Glycerol concentrations required for cryoprotection of 50 typical protein crystallization conditions." J. Appl. Cryst. (1996) 29, 584-587.
  • Garman E, Owen RL. "Cryocrystallography of macromolecules: practice and optimization." Methods Mol Biol. 2007;364:1-18.
  • Kriminski S, Kazmierczak M, Thorne RE. "Heat transfer from protein crystals: implications for flash-cooling and X-ray beam heating." Acta Crystallogr D. 2003, 59(4):697-708.
  • Hanson BL, Schall CA, Bunick GJ. "New techniques in macromolecular cryocrystallography: macromolecular crystal annealing and cryogenic helium." J Struct Biol. 2003, 142:77-87.
  • Harp JM, Timm DE, Bunick GJ. "Macromolecular crystal annealing: overcoming increased mosaicity associated with cryocrystallography." Acta Crystallogr D Biol Crystallogr. 1998 Jul 1;54(Pt 4):622-8.
  • Weik M, Ravelli RB, Silman I, Sussman JL, Gros P, Kroon J. "Specific protein dynamics near the solvent glass transition assayed by radiation-induced structural changes." Protein Sci. 2001, 10:1953-1961.
  • Rubinson KA, Ladner JE, Tordova M, Gilliland GL. "Cryosalts: suppression of ice formation in macromolecular crystallography." Acta Crystallogr D. 2000, 56:996-1001.
• Garman EF "Radiation damage in macromolecular crystallography: what is it and why should we care?" Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):339-51.
  • Barker AI, Southworth-Davies RJ, Paithankar KS, Carmichael I, Garman EF. "Room-temperature scavengers for macromolecular crystallography: increased lifetimes and modified dose dependence of the intensity decay." J Synchrotron Radiat. 2009 Mar;16(Pt 2):205-16.
  • Garman EF, Nave C. "Radiation damage in protein crystals examined under various conditions by different methods." J Synchrotron Radiat. 2009 Mar;16(Pt 2):129-32.
  • Ravelli RB, Garman EF. "Radiation damage in macromolecular cryocrystallography." Curr Opin Struct Biol. 2006 Oct;16(5):624-9.
  • Garman EF, Owen RL. "Cryocooling and radiation damage in macromolecular crystallography." Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):32-47.
  • Garman EF, Doublié S. "Cryocooling of macromolecular crystals: optimization methods." Methods Enzymol. 2003;368:188-216.
  • Garman E. "'Cool' crystals: macromolecular cryocrystallography and radiation damage." Curr Opin Struct Biol. 2003 Oct;13(5):545-51.
  • Weik M, Ravelli RB, Kryger G, McSweeney S, Raves ML, Harel M, Gros P, Silman I, Kroon J, Sussman JL. "Specific chemical and structural damage to proteins produced by synchrotron radiation." Proc Natl Acad Sci USA. 2000, 97:623-628.
• Garman E, Sweet RM. "X-ray data collection from macromolecular crystals." Methods Mol Biol. 2007;364:63-94.
• Garman EF. "Modern methods for rapid x-ray diffraction data collection from crystals of macromolecules." Methods Mol Biol. 1996, 56:87-126. (PDF)
• Gonzalez A. "Optimizing data collection for structure determination." Acta Crystallogr D. (2003) 59, 1935-1942.
• Kuo A, Bowler MW, Zimmer J, Antcliff JF, Doyle DA. "Increasing the diffraction limit and internal order of a membrane protein crystal by dehydration." J Struct Biol. 2003, 141:97-102.
  • Heras B, Edeling MA, Byriel KA, Jones A, Raina S, Martin JL. "Dehydration converts DsbG crystal diffraction from low to high resolution." Structure. 2003, 11:139-45.
  • Esnouf RM, Ren J, Garman EF, Somers DO, Ross CK, Jones EY, Stammers DK, Stuart DI. "Continuous and discontinuous changes in the unit cell of HIV-1 reverse transcriptase crystals on dehydration." Acta Crystallogr D. 1998, 54:938-953.
• Lusty CJ "A gentle vapor-diffusion technique for cross-linking of protein crystals for cryocrystallography" J. Appl. Cryst. 1999. 32:106-112.
We used a related method described vaguely in the following publication to stabilize especially environment-sensitive crystals of CDK6:INK4 complexes prior to mounting:
• Russo AA, Tong L, Lee JO, Jeffrey PD, Pavletich NP. "Structural basis for inhibition of the cyclin-dependent kinase Cdk6 by the tumour suppressor p16INK4a." Nature. 1998 Sep 17;395(6699):237-43.

Data Processing and Initial Analysis

• Leslie AG. "The integration of macromolecular diffraction data." Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):48-57.
Leslie AGW. "Recent changes to the MOSFLM package for processing film and image plate data." (1992), Joint CCP4 + ESF-EAMCB Newsletter on Protein Crystallography, No. 26.
• Otwinowski Z, Minor W. "Processing of X-ray Diffraction Data Collected in Oscillation Mode." Methods in Enzymology. 1997, Volume 276: Macromolecular Crystallography, part A, 307-326, C.W. Carter, Jr. & R. M. Sweet, Eds., Academic Press (New York).
• Kabsch W. "XDS." Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):125-32.
  • Kabsch W. "Integration, scaling, space-group assignment and post-refinement." Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):133-44.
• Winter G. "xia2: an expert system for macromolecular crystallography data reduction." J. Appl. Cryst. 2010, 43, 186-190.
• French GS, Wilson KS. Acta. Cryst. (1978), A34, 517.
• Lebedev AA, Vagin AA, Murshudov GN. "Intensity statistics in twinned crystals with examples from the PDB." Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):83-95.
• Zwart PH, Grosse-Kunstleve RW, Lebedev AA, Murshudov GN, Adams PD. "Surprises and pitfalls arising from (pseudo)symmetry." Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):99-107.

Experimental Phasing

MAX LIKELIHOOD ORIGINAL PHASING PAPERS (Blow etc)

• Blow DM, Crick FHC. "The treatment of errors in the isomorphous replacement method." Acta Cryst. 1959, 12, 794-802.
• Blow DM, Rossmann MG. "The single isomorphous replacement method." Acta Cryst. 1961, 14, 1195-1202.
• Hendrickson WA, Lattman EE. "Representation of Phase Probability Distributions for Simplified Combination of Independent Phase Information." Acta Cryst. 1970, B26, 136-143. (Hendrickson-Lattman coefficients, ABCD)
• Hendrickson WA. "Determination of macromolecular structures from anomalous diffraction of synchrotron radiation." Science. 1991 Oct 4;254(5028):51-8.
  • Hendrickson WA. "Analysis of Protein Structure from Diffraction Measurement at Multiple Wavelengths." Trans. ACA. 1985, 21, 11-21.
  • Hendrickson WA, Ogata CM "Phase Determination from Multiwavelength Anomalous Diffraction Measurements." Methods in Enzymology. 1997, 276, 494-523.
  • Terwilliger TC. "MAD Phasing: Bayesian Estimates of FA" Acta Cryst. 1994, D50, 11-16.
  • Terwilliger TC. "MAD Phasing: Treatment of Dispersive Differences as Isomorphous Replacement Information." Acta Cryst. 1994, D50, 17-23.
  • Pahler A, Smith JL, Hendrickson WA. "A Probability Representation for Phase Information from Multiwavelength Anomalous Dispersion." Acta Cryst. 1990, A46, 537-540.
  • Hendrickson WA, Smith JL, Phizackerley RP, Merritt EA. "Crystallographic structure analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation." Proteins. 1988;4(2):77-88.
  • Guss JM, Merritt EA, Phizackerley RP, Hedman B, Murata M, Hodgson KI, Freeman HC "Phase determination by multiple-wavelength X-ray diffraction: crystal structure of a basic blue copper protein from cucumbers." Science. 1989, 241, 806-811.
  • Smith JL. "Multiwavelength Anomalous Diffraction in Macromolecular Crystallography". CCP4 Conference Proceedings 1997.
  • Karle J "Some Developments in Anomalous Dispersion for the Structural Investigation of Macromolecular Systems in Biology". International Journal of Quantum Chemistry: Quantum Biology Symposium, 1980. 7, 357-367.
  • Karle J. "Linear Algebraic Analyses of Structures with One Predominant Type of Anomalous Scatterer". Acta Cryst. 1989, A45, 303-307.
  • Bella J, Rossmann MG "A General Phasing Algorithm for Multiple MAD and MIR Data." Acta Cryst. 1998, D54, 159-174.
  • Evans G. "The method of Multiple wavelength Anomalous Diffraction using Synchrotron Radiation at optimal X-ray energies: Application to Protein Crystallography." Ph.D. thesis, University of Warwick. 1994.
  • Boggon TJ, Shapiro L. "Screening for phasing atoms in protein crystallography." Structure 8, 2000. 8, R143-R149.
  • Hendrickson WA, Horton JR, LeMaster DM. "Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure." EMBO J. 1990, 9, 1665-1672.
  • Barton WA, Tzvetkova-Robev D, Erdjument-Bromage H, Tempst P, Nikolov DB "Highly efficient selenomethionine labeling of recombinant proteins produced in mammalian cells." Protein Sci. 2006, 15, 2008-2013.
• Dauter Z, Dauter M, Dodson E. "Jolly SAD." Acta Crystallogr D. 2002, 58:494-506.
  • Dodson E. "Is it jolly SAD ?" Acta Crystallogr D. 2003, 59:1958-1965.
  • Dauter Z. "One-and-a-half wavelength approach." Acta Crystallogr D. 2002, 58:1958-1967.
• McCoy AJ, Read RJ. "Experimental phasing: best practice and pitfalls." Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69
• Read RJ. "New ways of looking at experimental phasing." Acta Crystallogr D Biol Crystallogr. 2003 Nov;59(Pt 11):1891-902.
• Taylor G. "The phase problem." Acta Cryst. (2003). D59, 1881-1890. (CCP4 study weekend introductory material)
• Weeks CM, Adams PD, Berendzen J, Brünger AT, Dodson EJ, Grosse-Kunstleve RW, Schneider TR, Sheldrick GM, Terwilliger TC, Turkenburg MG, Uson I. Automatic solution of heavy-atom substructures." Methods Enzymol. 2003, 374:37-83.
• Schneider TR, Sheldrick GM. "Substructure solution with SHELXD." Acta Crystallogr D. 2002, 58:1772-1779.
  • Sheldrick GM. "Experimental phasing with SHELXC/D/E: combining chain tracing with density modification." Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):479-85.
  • Uson I, Schmidt B, von Bulow R, Grimme S, von Figura K, Dauter M, Rajashankar KR, Dauter Z, Sheldrick GM. Locating the anomalous scatterer substructures in halide and sulfur phasing." Acta Crystallogr D. 2003, 59:57-66.
  • Dall'Antonia F, Baker PJ, Schneider TR. "Optimization of selenium substructures as obtained from SHELXD." Acta Crystallogr D. 2003, 59:1987-1994.
• Grosse-Kunstleve RW, Brünger AT. "A highly automated heavy-atom search procedure for macromolecular structures. " Acta Crystallogr D. 1999, 55:1568-1577.
• Sun PD, Radaev S. "Generating isomorphous heavy-atom derivatives by a quick-soak method. Part II: phasing of new structures." Acta Crystallogr D. 2002, 58:1099-1103.
  • Sun PD, Radaev S, Kattah M. "Generating isomorphous heavy-atom derivatives by a quick-soak method. Part I: test cases." Acta Crystallogr D Biol Crystallogr. 2002 Jul;58(Pt 7):1092-8.
  • Garman E, Murray JW. "Heavy-atom derivatization." Acta Crystallogr D Biol Crystallogr. 2003 Nov;59(Pt 11):1903-13.
  • Yang C, Pflugrath JW, Courville DA, Stence CN, Ferrara JD. "Away from the edge: SAD phasing from the sulfur anomalous signal measured in-house with chromium radiation." Acta Crystallogr D. 2003, 59:1943-1957.
  • Yang C, Pflugrath JW. "Applications of anomalous scattering from S atoms for improved phasing of protein diffraction data collected at Cu Kalpha wavelength." Acta Crystallogr D. 2001, 57:1480-1490.
  • Beck T, Krasauskas A, Gruene T, Sheldrick GM "A magic triangle for experimental phasing of macromolecules." Acta Crystallogr. Section D 2008, 64, 1179-118 (PDF).
  • Beck T, da Cunha CE, Sheldrick GM. "How to get the magic triangle and the MAD triangle into your protein crystal." Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Oct 1;65(Pt 10):1068-70.
  • Morth JP, Sorensen TL, Nissen P "Membrane's Eleven: heavy-atom derivatives of membrane protein crystals". Acta Cryst. D 2006. 62, 877-882.
  • Retailleau P, Prange T. "Phasing power at the K absorption edge of organic arsenic." Acta Crystallogr D. 2003, 59:887-896.
• Bricogne G, Vonrhein C, Flensburg C, Schiltz M, Paciorek W. "Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0." Acta Crystallogr D Biol Crystallogr. 2003 Nov;59(Pt 11):2023-30.
  • Vonrhein C, Blanc E, Roversi P, Bricogne G. "Automated structure solution with autoSHARP." Methods Mol Biol. 2007;364:215-30.
  • de La Fortelle E, Irwin JJ, Bricogne G. "SHARP: A Maximum-Likelihood Heavy-Atom Parameter Refinement and Phasing Program for the MIR and MAD Methods" in Crystallographic Computing 7, Philip Bourne and Keith Watenpaugh, eds.
  • de la Fortelle E, Bricogne G. "Maximum-Likelihood Heavy-Atom Parameter Refinement for Multiple Isomorphous Replacement and Multiwavelength Anomalous Diffraction Methods." Methods in Enzymology, Macromolecular Crystallography Part A. 1997, 276, pp. 472-494.
• Terwilliger TC. "SOLVE and RESOLVE: automated structure solution and density modification." Methods Enzymol. 2003, 374:22-37.
  • Terwilliger T "SOLVE and RESOLVE: automated structure solution, density modification and model building" J. Synchrotron Rad. (2004). 11, 49-52
  • Terwilliger TC. "Statistical density modification using local pattern matching." Acta Crystallogr D. 2003, 59:1688-1701.
  • Terwilliger TC. "Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement." Acta Crystallogr D. 2003, 59:1174-1182.
  • Terwilliger TC, Berendzen J. "Automated MAD and MIR structure solution." Acta Crystallogr D. 1999, 55:849-861.
• Weeks CM, Miller R. "The design and implementation of SnB v2.0." J. Appl. Cryst. 1999. 32:120-124.
  • Xu H, Weeks CM, Deacon AM, Miller R, Hauptman, HA. "Ill-conditioned Shake-and-Bake: The trap of the false minimum." Acta Crystallogr A. 2000. 56:112-118.
• Furey W, Swaminathan S. "PHASES-95: A Program Package for the Processing and Analysis of Diffraction Data from Macromolecules." in Methods in Enzymology (Carter C, Sweet R eds) Academic Press, Orlando, Fl. 1995.
• Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD. "Automated structure solution with the PHENIX suite." Methods Mol Biol. 2008;426:419-35.
  • Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Zwart PH, Hung LW, Read RJ, Adams PD. "Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard." Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):61-9.
• Soltis SM, Stowell MHB, Wiener MC, Phillips GN, Rees DC. "Successful flash-cooling of xenon-derivatized myoglobin crystals." (pdf) J. Appl. Cryst. 1997, 30:190-194.
  • Panjikar S, Tucker PA. Phasing possibilities using different wavelengths with a xenon derivative." J. Appl. Cryst. 2002, 35, 261-266.
  • Cohen A, Ellis P, Kresge N, Soltis SM. "MAD phasing with krypton." Acta Crystallogr D. 2001, 57:233-238.
• Dauter Z, Dauter M, Rajashankar KR. "Novel approach to phasing proteins: derivatization by short cryo-soaking with halides." Acta Crystallogr D Biol Crystallogr. 2000 Feb;56(Pt 2):232-7.
  • Dauter Z. "New approaches to high-throughput phasing." Curr Opin Struct Biol. 2002, 12:674-678.
  • Dauter Z, Li M, Wlodawer A. "Practical experience with the use of halides for phasing macromolecular structures: a powerful tool for structural genomics." Acta Crystallogr D Biol Crystallogr. 2001. 57, 239-249.
• Gonzalez A, Pedelacq J, Sola M, Gomis-Ruth FX, Coll M, Samama J, Benini S. "Two-wavelength MAD phasing: in search of the optimal choice of wavelengths." Acta Crystallogr D. 1999, 55:1449-1458.
  • Teplyakov A, Oliva G, Polikarpov I. "On the choice of an optimal wavelength in macromolecular crystallography." Acta Crystallogr D. 1998, 54:610-614.
• Helliwell JR. "Overview and new developments in softer X-ray (2A < lambda < 5A) protein crystallography." J Synchrotron Radiat. 2004, 11:1-3.
• Yu-dong L, Harvey I, Yuan-xin G, Chao-de Z, Yi-zong H, Hai-fu F, Hasnain SS, Hao Q. "Is single-wavelength anomalous scattering sufficient for solving phases? A comparison of different methods for a 2.1 A structure solution." Acta Crystallogr D. 1999, 55:1620-1622.
• Rodríguez DD, Grosse C, Himmel S, González C, de Ilarduya IM, Becker S, Sheldrick GM, Usón I. "Crystallographic ab initio protein structure solution below atomic resolution." Nat Methods. 2009 Sep;6(9):651-3. Epub 2009 Aug 16.
  • Usón I, Sheldrick GM. "Advances in direct methods for protein crystallography." Curr Opin Struct Biol. 1999 Oct;9(5):643-8.

Molecular Replacement

• Rossman MG, Blow DM. "The Detection of Sub-Units within the Crystallographic Asymmetric Unit." Acta Cryst. 1962, 15, 24-32. (the Rotation Function)
• Crowther RA. "The fast rotation function." In The molecular replacement method. A collection of papers on the use of non-crystallographic symmetry (Ed, M.G., R.) Gordon and Breach, Science Publishers, Inc., New York, 1972, pp. 173-178. (the Fast Rotation Function)
• Rossmann MG, Blow DM. "A method of positioning a known molecule in an unknown crystal structure" Acta Cryst. 1967, 23, 544-548. (the Translation Functions T, T1 and T2)
• Harada Y, Lifschitz A, Berthou J, Jolles P. "A translation function combining packing and diffraction information: an application to lysozyme (high-temperature form)" Acta Cryst. 1981, A37, 398-406. (TO/O Translation Function) (PDF)
• Chen YW, Dodson EJ, Kleywegt GJ. "Does NMR mean "not for molecular replacement"? Using NMR-based search models to solve protein crystal structures." Structure. 2000 Nov 15;8(11):R213-20.
• McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. "Phaser crystallographic software." J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674. - definitive PHASER reference
  • McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ. "Likelihood-enhanced fast translation functions." Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64.
  • Storoni LC, McCoy AJ, Read RJ. "Likelihood-enhanced fast rotation functions." Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8.
  • Read RJ. "Pushing the boundaries of molecular replacement with maximum likelihood." Acta Crystallogr D Biol Crystallogr. 2001 Oct;57(Pt 10):1373-82.
  • McCoy AJ. "New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography." Curr Opin Struct Biol. 2002 Oct;12(5):670-3.
• Navaza J. "Implementation of molecular replacement in AMoRe." Acta Crystallogr D Biol Crystallogr. 2001 Oct;57(Pt 10):1367-72.
MOLREP
• Fitzgerald PMD. "MERLOT, an integrated package of computer programs for the determination of crystal structures by molecular replacement." J. Appl. Cryst. (1988). 21, 273-278
CROWTHER BLOW ROSSMAN BLOW TANAKA etc
• Grosse-Kunstleve RW, Adams PD. "Patterson correlation methods: a review of molecular replacement with CNS." Acta Crystallogr D Biol Crystallogr. 2001 Oct;57(Pt 10):1390-6.
• Tong L, Rossmann MG. "The locked rotation function." Acta Cryst. (1990). A46, 783-792. (PDF).
• Vagin A, Teplyakov A. "MOLREP: an Automated Program for Molecular Replacement." J. Appl. Cryst. (1997). 30, 1022-1025
• Long F, Vagin AA, Young P, Murshudov GN. "BALBES: a molecular-replacement pipeline." Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):125-32.

Density Modification

B-C Wang pioneered the use of solvent flattening to improve phase quality in experimental maps, dating from the early 1980's. Subsequently there have been many embellishments to the basic idea, to the point where it's an extremely powerful technique. (Need more references on Averaging, including things dating to the "Joy of Skewing").

• Wang BC. "Resolution of phase ambiguity in macromolecular crystallography." Methods Enzymol. 1985;115:90-112.
• Leslie AGW. "A reciprocal-space method for calculating a molecular envelope using the algorithm of B.C. Wang." Acta Cryst. 1987, A43, 134-136.
• Zhang KYJ, Cowtan K, Main P. "Combining constraints for electron-density modification." Methods in Enzymol. 1997, 277, 53-64.
• Abrahams JP, Leslie AGW. "Methods used in the structure determination of bovine mitochondrial F1 ATPase." Acta Cryst. 1996, D52, 30-42. (PDF)
• Cowtan K. "'dm': An automated procedure for phase improvement by density modification." Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography. 1994, 31, p4-38.
• Cowtan KD, Main P. "Phase combination and cross validation in iterated density-modification calculations." Acta Cryst. 1996, D52, 43-48.
• Zhang KYJ. "SQUASH - combining constraints for macromolecular phase refinement and extension" Acta Cryst. (1993). D49, 213-222.
• Kleywegt GJ, Jones TA. "Software for handling macromolecular envelopes."
• Kleywegt GJ, Read RJ. "Not your average density." Structure. 1997 Dec 15;5(12):1557-69. PDF
• Langer G, Cohen SX, Lamzin VS, Perrakis A. "Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7." Nat Protoc. 2008;3(7):1171-9.
  • Joosten K, Cohen SX, Emsley P, Mooij W, Lamzin VS, Perrakis A. "A knowledge-driven approach for crystallographic protein model completion." Acta Crystallogr D Biol Crystallogr. 2008 Apr;64(Pt 4):416-24.
  • Cohen SX, Ben Jelloul M, Long F, Vagin A, Knipscheer P, Lebbink J, Sixma TK, Lamzin VS, Murshudov GN, Perrakis A. "ARP/wARP and molecular replacement: the next generation." Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):49-60.

Refinement

• Brünger AT. "Free R value: a novel statistical quantity for assessing the accuracy of crystal structures." Nature. 1992. 355, 472-475.
  • Brünger AT. "Assessment of phase accuracy by cross validation: the free R value. Methods and applications." Assessment of phase accuracy by cross validation: the free R value. Methods and applications.
  • Brünger AT. "The free R value: a more objective statistic for crystallography." Methods Enzymol. 1997. 277, 366-396.
  • Tickle IJ, Laskowski RA, Moss DS. "Rfree and the rfree ratio. II. Calculation Of the expected values and variances of cross-validation statistics in macromolecular least-squares refinement." Acta Crystallogr D Biol Crystallogr. 2000 Apr;56(Pt 4):442-50.
  • Tickle IJ, Laskowski RA, Moss DS. "Rfree and the Rfree Ratio. I. Derivation of Expected Values of Cross-Validation Residuals Used in Macromolecular Least-Squares Refinement" Acta Cryst. (1998). D54, 547-557
  • Kleywegt GJ. "Separating model optimization and model validation in statistical cross-validation as applied to crystallography." Acta Crystallogr D Biol Crystallogr. 2007 Sep;63(Pt 9):939-40.
• Kleywegt GJ, Jones TA. "Model building and refinement practice." Methods Enzymol. 1997;277:208-30.
• Kuriyan J, Brünger AT, Karplus M, Hendrickson WA. "X-ray refinement of protein structures by simulated annealing: test of the method on myohemerythrin." Acta Crystallogr A. 1989 Jun 1;45 ( Pt 6):396-409.
  • Brünger AT. "Crystallographic refinement by simulated annealing. Application to a 2.8 A resolution structure of aspartate aminotransferase." J Mol Biol. 1988 Oct 5;203(3):803-16.
  • Weis WI, Brünger AT, Skehel JJ, Wiley DC. "Refinement of the influenza virus hemagglutinin by simulated annealing." J Mol Biol. 1990 Apr 20;212(4):737-61.
• Kleywegt GJ. "Use of non-crystallographic symmetry in protein structure refinement." Acta Crystallogr D Biol Crystallogr. 1996 Jul 1;52(Pt 4):842-57.
• Jiang JS, Brünger AT "Protein hydration observed by X-ray diffraction. Solvation properties of penicillopepsin and neuraminidase crystal structures." J Mol Biol. 1994 Oct 14;243(1):100-15.
  • Fokine A, Urzhumtsev A "Flat bulk-solvent model: obtaining optimal parameters". Acta Crystallogr D Biol Crystallogr. 2002 Sep;58(Pt 9):1387-92. Epub 2002 Aug 23.
  • Afonine PV, Grosse-Kunstleve RW, Adams PD. "A robust bulk-solvent correction and anisotropic scaling procedure" Acta Crystallogr D Biol Crystallogr. 2005 Jul;61(Pt 7):850-5.
• Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. "Crystallography & NMR system: A new software suite for macromolecular structure determination." Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21. definitive CNS reference
  • Brünger AT. "Version 1.2 of the Crystallography and NMR system." Nat Protoc. 2007;2(11):2728-33. secondary CNS reference
• Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. "PHENIX: a comprehensive Python-based system for macromolecular structure solution." Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. - definitive PHENIX reference
• Murshudov GN, Vagin AA, Dodson EJ. "Refinement of macromolecular structures by the maximum-likelihood method." Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55. - probably definitive REFMAC reference
  • Skubák P, Murshudov GN, Pannu NS. "Direct incorporation of experimental phase information in model refinement." Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2196-201.
  • Winn MD, Murshudov GN, Papiz MZ. "Macromolecular TLS refinement in REFMAC at moderate resolutions." Methods Enzymol. 2003;374:300-21.
  • Winn MD, Isupov MN, Murshudov GN. "Use of TLS parameters to model anisotropic displacements in macromolecular refinement." Acta Crystallogr D Biol Crystallogr. 2001 Jan;57(Pt 1):122-33.
• Kleywegt GJ, Jones TA. "Efficient rebuilding of protein structures." Acta Crystallogr D Biol Crystallogr. 1996 Jul 1;52(Pt 4):829-32.
• Luzzati, V. "Traitement statistique des erreurs dans la determination des structures cristallines." Acta Cryst. 1952, 5, 802-810.
• Müller P, Köpke S, Sheldrick GM "Is the bond-valence method able to identify metal atoms in protein structures?" Acta Cryst. (2003). D59, 32-37

Validation

Since people on occasion completely mess up their structures or make more subtle pernicious errors that are less obvious, validation has emerged as a critical component of structure determination. The papers of Gerard Kleywegt are always worth a read, as they pull few punches. The first three in this list, the "angry young men" articles, are mandatory. Validation software helps a lot too: PROCHECK in the early days, MOLPROBITY more recently, possibly aided and abetted by POLYGON.

• Kleywegt GJ, Jones TA. "Where freedom is given, liberties are taken." Structure. 1995 Jun 15;3(6):535-40.
  • Kleywegt GJ, Brünger AT. "Checking your imagination: applications of the free R value." Structure. 1996 Aug 15;4(8):897-904. PDF.
  • Kleywegt GJ, Jones TA. "Phi/psi-chology: Ramachandran revisited." Structure. 1996 Dec 15;4(12):1395-400. PDF.
  • Jones TA, Kleywegt GJ. "Experimental data for structure papers." Science. 2007 Jul 13;317(5835):194-5.
  • Kleywegt GJ, Jones TA. "Homo crystallographicus--quo vadis?" Structure. 2002 Apr;10(4):465-72.
  • Read RJ, Kleywegt GJ. "Case-controlled structure validation." Acta Crystallogr D Biol Crystallogr. 2009 Feb;65(Pt 2):140-7.
  • Kleywegt GJ. "On vital aid: the why, what and how of validation." Acta Crystallogr D Biol Crystallogr. 2009 Feb;65(Pt 2):134-9.
  • Kleywegt GJ. "Validation of protein crystal structures." Acta Crystallogr D Biol Crystallogr. 2000 Mar;56(Pt 3):249-65.
  • Kleywegt GJ. "Quality control and validation." Methods Mol Biol. 2007;364:255-72.
  • Kleywegt GJ, Harris MR. "ValLigURL: a server for ligand-structure comparison and validation." Acta Crystallogr D Biol Crystallogr. 2007 Aug;63(Pt 8):935-8.
• Branden CI, Jones TA "Between objectivity and subjectivity." Nature. 1990. 343, 687-689.
• The use of R-free during refinement (see up in the Refinement section for refs) is a critical tool for validation
• Ramachandran GN, Ramakrishnan C, Sasisekharan V. "Stereochemistry of polypeptide chain configurations." J Mol Biol. 1963. 7, 95-99.
• Dodson EJ, Davies GJ, Lamzin VS, Murshudov GN, Wilson KS. "Validation tools: can they indicate the information content of macromolecular crystal structures?" Structure. 1998 Jun 15;6(6):685-90.
• Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. "MolProbity: all-atom structure validation for macromolecular crystallography." Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):12-21.
• Laskwoski RA, MacArthur MW, Moss DS, Thornton JM. "PROCHECK: a program to check the stereochemical quality of protein structures." J. Appl. Cryst. (1993). 26, 283-291 .
• Urzhumtseva L, Afonine PV, Adams PD, Urzhumtsev A. "Crystallographic model quality at a glance." Acta Crystallogr D Biol Crystallogr. 2009 Mar;65(Pt 3):297-300.
• Vaguine AA, Richelle J, Wodak SJ. "SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model." Acta Crystallogr. 1999. D55, 191-20.

Graphics

• Jones TA, Zou JY, Cowan SW, Kjeldgaard M. "Improved methods for building protein models in electron density maps and the location of errors in these models." Acta Cryst. 1991, A47, 110-119.
• Emsley P, Cowtan K "Coot: model-building tools for molecular graphics" Acta Cryst. (2004). D60, 2126-2132
• Kraulis PJ "MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures." J. Appl. Cryst. (1991). 24, 946-950
• Carson M. "Ribbons." Methods in Enzymology, Macromolecular Crystallography. 1997, 277, 493-505. (HTML)
  • Carson M. "Ribbons 2.0." J.Appl.Cryst. 1991, 24, 958-961. (HTML) (PDF)
• Potterton E, McNicholas S, Krissinel E, Cowtan K, Noble M. "The CCP4 molecular-graphics project." Acta Crystallogr D. 2002. 58:1955-1957.
• PyMol doesn't seem to have a literature reference.
• Greer J. "Three-dimensional pattern recognition: an approach to automated interpretation of electron density maps of proteins." J. Mol. Biol. 1974, 82, 279-301.

Databases

To add: CSD.

• Bernstein FC, Koetzle TF, Williams GJ, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. "The Protein Data Bank: a computer-based archival file for macromolecular structures." J Mol Biol. 1977 May 25;112(3):535-42.
• Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C. "The Protein Data Bank." Acta Crystallogr D Biol Crystallogr. 2002 Jun;58(Pt 6 No 1):899-907.

Miscellany

• Fang FC, Steen RG, Casadevall A. "Misconduct accounts for the majority of retracted scientific publications" Proc. Natl. Acad. Sci. USA 2012 Oct;109(42):17028-17033.

(There are some notable exceptions to this within structural biology, including the whole MsbA/EmrE saga).

Content © Phil Jeffrey. Contact me at: phil.jeffrey~at~gmail.com