Up: User's Guide to Macromolecular Crystallography Experiments
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Subsections
Further reading
If you want to read more about beamlines, data collection strategy,
phasing and structure refinement methods and software, please consult
the list of references
below. For additional information about methods and programs
used for data collection and processing at SSRL, please see the
references to supported software/hardware
General
Mitchell E, Kuhn P, Garman E. Demystifying the synchrotron trip: a first time user's guide. Structure Fold Des. 1999, 7:R111-121.
Nave C. Matching X-ray source, optics and detectors to protein crystallography requirements. Acta Crystallogr D Biol Crystallogr. 1999, 55:1663-1668.
Automation
Abola E, Kuhn P, Earnest T, Stevens RC. Automation of X-ray crystallography. Nat Struct Biol. 2000, 7 Suppl:973-977.
Detectors
ADSC
http://www.adsc-xray.com/products.html
MarResearch
http://www.marresearch.com/
Derivatives
Garman E, Murray JW. Heavy-atom derivatization. Acta Crystallogr D. 2003, 59:1903-1913.
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.
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.
Garman E. Leaving no element of doubt: analysis of proteins using microPIXE. Structure Fold Des. 1999, 7:R291-299.
Soltis SM, Stowell MHB, Wiener MC, Phillips GN, Rees DC. Successful flash-cooling of xenon-derivatized myoglobin crystals J. Appl. Cryst. 1997, 30:190-194.
Rigaku/MSC CryoX-siter
http://www.msc.com/protein/application_notes/CryoXe-AppNote.pdf
Data collection
Gonzalez A. Optimizing data collection for structure determination. Acta Crystallogr D. 2003, 59:1935-1942.
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.
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.
Garman EF. Modern methods for rapid x-ray diffraction data collection from crystals of macromolecules. Methods Mol Biol. 1996, 56:87-126.
MAD/SAD
Helliwell JR. Overview and new developments in softer X-ray (2A < lambda < 5A) protein crystallography. J Synchrotron Radiat. 2004, 11:1-3.
Giacovazzo C, Siliqi D. Phasing via SAD/MAD data: the method of the joint probability distribution functions. Acta Crystallogr D. 2004, 6:73-82.
Dall'Antonia F, Baker PJ, Schneider TR. Optimization of selenium substructures as obtained from SHELXD. Acta Crystallogr D. 2003, 59:1987-1994.
Dodson E. Is it jolly SAD? Acta Crystallogr D. 2003, 59:1958-1965.
Retailleau P, Prange T. Phasing power at the K absorption edge of organic arsenic. Acta Crystallogr D. 2003, 59:887-896.
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.
Weeks CM, Adams PD, Berendzen J, Brunger 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.
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.
Dauter Z. New approaches to high-throughput phasing. Curr Opin Struct Biol. 2002, 12:674-678.
Dauter Z. One-and-a-half wavelength approach. Acta Crystallogr D. 2002, 58:1958-1967.
Dauter Z, Dauter M, Dodson E. Jolly SAD. Acta Crystallogr D. 2002, 58:494-506.
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.
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.
Crystallographic
software (phasing and
refinement)
Morris RJ, Perrakis A, Lamzin VS (2002) ARP/wARP's model-building algorithms. I. The main chain. Acta Crystallogr D. 2002, 58:968-975. http://www.embl-hamburg.de/ARP/
Perrakis A, Harkiolaki M, Wilson KS, Lamzin VS. ARP/wARP and molecular replacement. Acta Cryst D. 2001, 57:1445-145.
Perrakis A, Morris RM, Lamzin VS. Automated protein model building combined with iterative structure refinement. Nature Struct Biol. 1999, 6:458-463.
Perrakis A, Sixma TK, Wilson KS, Lamzin VS. wARP: improvement and extension of crystallographic phases by weighted averaging of multiple refined dummy atomic models. Acta Cryst D. 1997, 53:448-455.
Potterton E, Briggs P, Turkenburg M, Dodson E. A graphical user interface to the CCP4 program suite. Acta Crystallogr D. 2003, 59(7):1131-1137. http://www.ccp4.ac.uk/main.html
Steiner RA, Lebedev AA, Murshudov GN. Fisher's information in maximum-likelihood macromolecular crystallographic refinement. Acta Crystallogr D. 2003, 59:2114-2124.
Winn MD. An overview of the CCP4 project in protein crystallography: an example of a collaborative project. J Synchrotron Radiat. 2003, 10:23-25.
Potterton E, McNicholas S, Krissinel E, Cowtan K, Noble M. The CCP4 molecular-graphics project. Acta Crystallogr D. 2002, 58:1955-1957.
Winn MD, Ashton AW, Briggs PJ, Ballard CC, Patel P. Ongoing developments in CCP4 for high-throughput structure determination. Acta Crystallogr D. 2002, 58:1929-1936.
Winn MD, Isupov MN, Murshudov GN. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr D. 2001, 57:122-133.
Murshudov GN, Vagin AA, Lebedev A, Wilson KS, Dodson EJ. Efficient anisotropic refinement of macromolecular structures using FFT. Acta Crystallogr D. 1999, 55:247-255.
Pannu NS, Murshudov GN, Dodson EJ, Read RJ. Incorporation of prior phase information strengthens maximum-likelihood structure refinement. Acta Crystallogr D. 1998, 54:1285-1294.
Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D. 1999, 53:240-255.
Brunger 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. 1998, 54: 905-921. http://cns.csb.yale.edu/v1.1/
Adams PD, Grosse-Kunstleve RW, Brunger AT. Computational aspects of high-throughput crystallographic macromolecular structure determination. Methods Biochem Anal. 2003, 44:75-87.
Brunger AT, Adams PD. Molecular dynamics applied to X-ray structure refinement. Acc Chem Res. 2002, 35:404-412.
Grosse-Kunstleve RW, Brunger AT. A highly automated heavy-atom search procedure for macromolecular structures. Acta Crystallogr D. 1999, 55:1568-1577.
Levitt DG. A New Software Routine that Automates the Fitting of Protein X-Ray Crystallographic Electron Density Maps. Acta Crystallgr D. 2001, 57:1013-1019. http://www.msi.umn.edu/ levitt/
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. http://www.imsb.au.dk/ mok/phases/phases.html
Schneider TR, Sheldrick GM. Substructure solution with SHELXD. Acta Crystallogr D. 2002, 58:1772-1779. http://shelx.uni-ac.gwdg.de/SHELX/
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. http://babinet.globalphasing.com/sharp/
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. 2003, 59:2023-2030.
Weeks, C.M. & Miller, R. The design and implementation of SnB v2.0, J. Appl. Cryst. 1999, 32:120-124. http://www.hwi.buffalo.edu/SnB/
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
Terwilliger TC, Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr D. 1999, 55:849-861.
Terwilliger TC. SOLVE and RESOLVE: automated structure solution and density modification. Methods Enzymol. 2003, 374:22-37. http://www.solve.lanl.gov/
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. Statistical density modification using local pattern matching. Acta Crystallogr D. 2003, 59:1688-1701.
Radiation damage
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.
Sliz P, Harrison SC, Rosenbaum G. How does radiation damage in protein crystals depend on X-ray dose? Structure. 2003, 11:13-19.
O'Neill P, Stevens DL, Garman EF. Physical and chemical considerations of damage induced in protein crystals by synchrotron radiation: a radiation chemical perspective. J Synchrotron Radiat. 2002, 9:329-332.
Garman E, Nave C. Radiation damage to crystalline biological molecules: current view. J Synchrotron Radiat. 2002, 9:327-328.
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.
Crystal dehydration
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.
Cryocrystallography
Garman EF, Doublie 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, 13:545-551.
Hanson BL, Schall CA, Bunick GJ. New techniques in macromolecular cryocrystallography: macromolecular crystal annealing and cryogenic helium. J Struct Biol. 2003, 142:77-87.
Snell EH, Judge RA, Larson M, van der Woerd MJ. Seeing the heat - preliminary studies of cryocrystallography using infrared imaging. J Synchrotron Radiat. 2002, 9:361-367.
Murray J, Garman E. Investigation of possible free-radical scavengers and metrics for radiation damage in protein cryocrystallography. J Synchrotron Radiat. 2002, 9:347-354.
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 E. Cool data: quantity AND quality. Acta Crystallogr D. 1999, 55:1641-1653.
Rodgers DW. Cryocrystallography. Structure. 1994, 2:1135-1140.
Hope H. Cryocrystallography of biological macromolecules: a generally applicable method. Acta Crystallogr B. 1988, 44:22-26.
Crystal annealing
Kriminski S, Caylor CL, Nonato MC, Finkelstein KD, Thorne RE. Flash-cooling and annealing of protein crystals. Acta Crystallogr D. 2002, 58:459-471.
Weik M, Kryger G, Schreurs AM, Bouma B, Silman I, Sussman JL, Gros P, Kroon J. Solvent behaviour in flash-cooled protein crystals at cryogenic temperatures. Acta Crystallogr D. 2001, 57:566-573.
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.
Harp JM, Timm DE, Bunick GJ. Macromolecular crystal annealing: overcoming increased mosaicity associated with cryocrystallography. Acta Crystallogr D. 1998, 54:622-628.
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