Crystals, X-rays and Proteins: Comprehensive Protein Crystallography

Crystals, X-rays and Proteins: Comprehensive Protein Crystallography

Volumn 9780199559046, Issue , 2011, Pages 1-640

  Sherwood, Dennis ^a   Cooper, Jon ^b  

^a The Silver Bullet Machine Manufacturing Company   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Diffraction; Electron density; Fourier transform; Proteins; Refinement; Solving the phase problem; Symmetry; X ray crystallography

Indexed keywords

BINDING SITES; CARRIER CONCENTRATION; CRYSTAL STRUCTURE; CRYSTAL SYMMETRY; DIFFRACTION; ELECTRON DENSITY MEASUREMENT; FOURIER TRANSFORMS; MOLECULES; PROTEINS; X RAYS;

DIFFRACTION METHODS; MOLECULAR REPLACEMENTS; PATTERSON FUNCTIONS; PHASE PROBLEM; PROTEIN CRYSTALLOGRAPHY; REFINEMENT; STRUCTURE ANALYSIS; X-RAY DATA COLLECTION;

X RAY CRYSTALLOGRAPHY;

EID: 84880546524     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1093/acprof:oso/9780199559046.001.0001     Document Type: Book

References (290)

1. Adachi, M., Ohhara, T., Kurihara, K., Tamada, T., Honjo, E., Okazaki, N., Arai, S., Shoyama, Y., Kimura, K., Matsumura, H., Sugiyama, S., Adachi, H., Takano, K., Mori, Y., Hidaka, K., Kimura, T., Hayashi, Y., Kiso, Y. and Kuroki, R. (2009) Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography. Proc. Natl. Acad. Sci. USA 106, 4641-6.
2. Adams, P. D., Mustyakimov, M., Afonine, P. V. and Langan, P. (2009) Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules. Acta Crystallogr. D 65, 567-;73.
3. Amemiya, Y. and Miyahara, J. (1988) Imaging plate illuminates many fields. Nature 336, 89-90.
4. Bacon, G. E. (1962) Neutron Diffraction, 2nd edn. Oxford University Press, London.
5. Bennett, B., Langan, P., Coates, L., Mustyakimov, M., Schoenborn, B., Howell, E. E. and Dealwis, C. (2006) Neutron diffraction studies of Escherichia coli dihydrofolate reductase complexed with methotrexate. Proc. Natl. Acad. Sci. USA 103, 18493-8.
6. Blakeley, M. P., Kalb, A. J., Helliwell, J. R. and Myles, D. A. (2004) The 15-K neutron structure of saccharide-free concanavalin A. Proc. Natl. Acad. Sci. USA 101, 16405-10.
7. Blakeley, M. P., Langan, P., Niimura, N. and Podjarny, A. (2008) Neutron crystal lography:opportunities, challenges, and limitations. Curr. Opin. Struct. Biol. 18, 593-600.
8. Blum, M.-M., Mustyakimov, M., Rüterjans, H., Kehe, K., Schoenborn, B. P., Langan, P. and Chen, J. C.-H. (2009) Rapid determination of hydrogen positionsand protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement. Proc. Natl. Acad. Sci. USA 106, 713-18.
9. Bon, C., Lehmann, M. S. and Wilkinson, C. (1999) Quasi-Laue neutron diffraction study of the water arrangement in crystals of triclinic lysozyme from hen egg-white. Acta Crystallogr. D 55, 978-87.
10. Bourgeois, D., Schotte, F., Brunori, M. and Vallone, B. (2007) Time-resolved methods in biophysics. 6. Time-resolved Laue crystallography as a tool to investigate photo-activated protein dynamics. Photochem. Photobiol. Sci. 6, 1047-56.
11. Burmeister, W. P. (2000) Structural changes in a cryo-cooled protein crystal owing to radiation damage. Acta Crystallogr. D 56, 328-41.
12. Cipriani, F., Castagna, J. C., Wilkinson, C., Oleinek, P. and Lehmann, M. S. (1996) Cold neutron protein crystallography using a large position-sensitive detector based on imageplate technology. J. Neutron Res. 4, 79-85.
13. Cleland, W. W., Frey, P. A. and Gerlt, J. A. (1998) The low-barrier hydrogen bond in enzymatic catalysis. J. Biol. Chem. 273, 25529-32.
14. Coates, L., Erskine, P. T., Wood, S. P., Myles, D. A. A. and Cooper, J. B. (2001) A neutron Laue diffraction study of endothiapepsin: implications for the aspartic proteinase mechanism. Biochemistry 40, 13149-57.
15. Coates, L., Tuan, H.-F., Tomanicek, S., Kovalevsky, A., Mustyakimov, M., Erskine, P. T. and Cooper, J. B. (2008) The catalytic mechanism of an aspartic proteinase explored with neutron and X-ray diffraction. J. Am. Chem. Soc. 130, 7235-7.
16. Ding, X., Rasmussen, B. F., Petsko, G. A. and Ringe, D. (1994) Direct structural observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase. Biochemistry 33, 9285-93.
17. Habash, J., Raftery, J., Weisgerber, S., Cassetta, A., Lehmann, M. S., Hoghoj, P., Wilkinson, C., Campbell, J. W. and Helliwell, J. R. (1997) Neutron Laue diffraction study of concanavalin A: the proton of Asp 28. J. Chem. Soc. Faraday Trans. 93, 4313-17.
18. Habash, J., Raftery, J., Nuttall, R., Price, H. J., Wilkinson, C., Kalb (Gilboa), A. J. and Helliwell, J. R. (2000) Direct determination of the positions of the deuterium atoms of the bound water in concanavalin A by neutron Laue crystallography. Acta Crystallogr. D 56, 541-50.
19. Hazemann, I., Dauvergne, M. T., Blakeley, M. P., Meilleur, F., Haertlein, M., Van Dorsselaer, A., Mitschler, A., Myles, D. A. A. and Podjarny, A. (2005) High-resolution neutron protein crystallography with radically small crystal volumes: application of perdeuteration to human aldose reductase. Acta Crystallogr. D 61, 1413-17.
20. Helliwell, J. R. (1992) Macromolecular Crystallography with Synchrotron Radiation. Cambridge University Press, Cambridge.
21. Helliwell, J. R., Price, H. J., Deacon, A., Raftery, I. and Habash, J. (2002) Complementarity of neutron and ultrahigh resolution synchrotron X-ray protein crystallography studies:results with concanavalin A at cryo and room temperature. Acta Physica Polonica A 101, 583-8.
22. Kossiakoff, A. A. (1983) Neutron protein crystallography: advances in methods and applications. Ann. Rev. Biophys. Bioeng. 12, 159-82.
23. Kossiakoff, A. A. and Spencer, S. A. (1980) Neutron diffraction identifies His 57 as the catalytic base in trypsin. Nature 288, 414-16.
24. Langan, P., Greene, G. and Schoenborn, B. P. (2004) Protein crystallography with spallation neutrons: the user facility at Los Alamos Neutron Science Center. J. Appl. Crystallogr. 37, 24-31.
25. Langan, P., Fisher, Z., Kovalevsky, A., Mustyakimov, M., Sutcliffe Valone, A., Unkefer, C., Waltman, M. J., Coates, L., Adams, P. D., Afonine, P. V., Bennett, B., Dealwis, C. and Schoenborn, B. P. (2008) Protein structures by spallation neutron crystallography. J. Synchrotron Radiation 15, 215-18.
26. Mason, S., Bentley, G. A. and McIntyre, G. (1984) Deuterium exchange in lysozyme at 1.4 Å resolution. In Neutrons in Biology, ed. Schoenborn, B. Plenum, New York, pp. 323-34.
27. Messerschmidt, A. (2007) X-ray Crystallography of Biomacromolecules: A Practical Guide. Wiley-VCH, Weinheim.
28. Myles, D. A. A. (2006) Neutron protein crystallography: current status and a brighter future. Curr. Opin. Struct. Biol. 16, 630-7.
29. Myles, D. A. A., Bon, C., Langan, P., Cipriani, F., Castagna, J. C., Lehmann, M. S. and Wilkinson, C. (1998) Neutron Laue diffraction in macromolecular crystallography. Physica B, 241, 1122-30.
30. Niimura, N., Minezaki, Y., Nonaka, T., Castagna, J. C., Cipriani, F., Hoghoj, P., Lehmann, M. S. and Wilkinson, C. (1997) Neutron Laue diffractometry with an imaging plate provides an effective data collection regime for neutron protein crystallography. Nature Struct. Biol. 4, 909-14.
31. Petit-Haertlein, I., Blakeley, M. P., Howard, E., Hazemann, I., Mitschler, A., Haertlein, M. and Podjarny, A. (2009) Perdeuteration, purification, crystallization and preliminary neutron diffraction of an ocean pout type III antifreeze protein. Acta Crystallogr. F 65, 406-409.
32. Rasmussen, B. F., Stock, A. M., Ringe, D. and Petsko, G. A. (1992) Crystalline ribonuclease A loses function below the dynamical transition at 220 K. Nature 357, 423-4.
33. Ravelli, R. B. G. and McSweeney, S. M. (2000) The fingerprint that X-rays leave on structures. Structure 8, 315-28.
34. Ravelli, R. B. G., Hezemans, A. M. F., Krabbendam, H. and Kroon, J. (1996) Towards automatic indexing of the Laue diffraction pattern. J. Appl. Crystallogr. 29, 270-8.
35. Schoenborn, B. (1994) Neutrons in Biology, Basic Life Sciences. Volume 27, Plenum, New York.
36. Schultz, A. J., Thiyagarajan, P., Hodges, J. P., Rehm, C., Myles, D. A. A., Langan, P. and Mesecar, A. D. (2005) Design of the next generation neutron macromolecular diffractometer at the spallation neutron source. J. Appl. Crystallogr. 38, 964-74.
37. Stoddard, B. L. (1998) New results using Laue diffraction and time-resolved crystallography. Curr. Opin. Struct. Biol. 8, 612-18.
38. Tanaka, I., Kusaka, K., Tomoyori, K., Niimura, N., Ohhara, T., Kurihara, K., Hosoya, T. and Ozekic, T. (2009) Overview of a new biological neutron diffrac-tometer (iBIX) in J-PARC. Nucl. Instrum. Methods Phys. Res. A. 600, 161-3.
39. Teixeira, S. C. M., Zaccai, G., Ankner, J., Bellissent-Funel, M. C., Bewley, R., Blakeley, M. P., Callow, P., Coates, L., Dahint, R., Dalgliesh, R., Dencher, N. A., Forsyth, V. T., Fragneto, G., Frick, B., Gilles, R., Gutberlet, T., Haertlein, M., Hauß, T., Häußler, W., Heller, W. T., Herwig, K., Holderer, O., Juranyi, F., Kampmann, R., Knott, R., Krueger, S., Langan, P., Lechner, R. E., Lynn, G., Majkrzak, C., May, R. P., Meilleur, F., Mo, Y., Mortensen, K., Myles, D. A. A., Natali, F., Neylon, C., Niimura, N., Ollivier, J., Ostermann, A., Peters, J., Pieper, J., Rühm, A., Schwahn, D., Shibata, K., Soper, A. K., Strßssle, T., Suzuki, J., Tanaka, I., Tehei, M., Timmins, P., Torikai, N., Unruh, T., Urban, V., Vavrin R. and Weiss, K. (2008) New sources and instrumentation for neutrons in biology. Chemical Physics 345, 133-51.
40. Tilton, R. F., Jr, Dewan, J. C. and Petsko, G. A. (1992) Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320K. Biochemistry 31, 2469-81.
41. Wilson, C. C. (2001) Hydrogen atoms in acetylsalicylic acid (aspirin): the librating methyl group and probing the potential well in the hydrogen bonded dimer. Chem. Phys. Lett. 335, 57-63.
42. Wlodawer, A. and Hendrickson, W. A. (1982) A procedure for joint refinement of macromolecular structures with X-ray and neutron diffraction data from single crystals. Acta Crystallogr. A 38, 239-47.
43. Wlodawer, A., Miller, M. and Sjolin, L. (1983) Active site of RNase-neutron diffraction study of a complex with uridine vanadate, a transition state analogue. Proc. Natl. Acad. Sci. USA 80, 3628-31.
44. Bishop, A. C. An Outline of Crystal Morphology. Hutchinson, London, 1967.
45. Buerger, M. J. Elementary Crystallography. Wiley, New York, 1963.
46. Cantor, C. R. and Schimmel, P. R. Biophysical Chemistry, Part II: Techniques for the Study of Biological Structure and Function. Freeman, San Francisco, 1980.
47. Phillips, F. C. An Introduction to Crystallography. Longman, London, 1971.
48. Stout, G. H. and Jensen, L. H. X-ray Structure Determination: A Practical Guide, 2nd edn. Wiley, New York, 1989.
49. International Tables for Crystallography. Volume A: Space-Group Symmetry. International Union of Crystallography, Chester, UK, 2005.
50. Born, M. and Wolf, E. Principles of Optics: Electromagnetic Theory of Propagation, Interference and Diffraction of Light, 7th edn. Cambridge University Press, Cambridge, 1999.
51. Jenkins, F. A. and White, H. E. Fundamentals of Optics, 4th edn. McGraw-Hill, New York, 1976.
52. Longhurst, R. S. Geometrical and Physical Optics. Longman, London, 1986.
53. Stone, J. M.Radiation and Optics. McGraw-Hill, New York, 1963.
54. Goodman, J. W. An Introduction to Fourier Optics. Roberts, Greenwood Village, CO, 2004.
55. Taylor, C. A. and Lipson, H. Optical Transforms. Bell, London, 1964.
56. Braddick, H. J. J. Vibrations, Waves and Diffraction. McGraw-Hill, London, 1965.
57. Francon, M.Diffraction-Coherence in Optics. Pergamon, New York, 1966.
58. Longhurst, R. S. Geometrical and Physical Optics, 2nd edn. Longman, London, 1986.
59. Amemiya, Y. and Miyahara, J. (1988) Imaging plate illuminates many fields. Nature 336, 89-90.
60. Arndt, U. W., Champness, J. N., Phizackerley, R. P. and Wonacott, A. J. (1973) A singlecrystal oscillation camera for large unit cells. J. Appl. Crystallogr. 6, 457-463.
61. Blessing, R. H. (1995) An empirical correction for absorption anisotropy. Acta Crystallogr. A 51, 33-8.
62. Bloomer, A. C. and Arndt, U. W. (1999) Experiences and expectations of a novel X-ray microsource with focusing mirror. Acta Crystallogr. 55, 1672-80.
63. Bourgeois, D., Schotte, F., Brunori, M. and Vallone, B. (2007) Time-resolved Laue crystallography as a tool to investigate photo-activated protein dynamics. Pho-tochem. Photobiol. Sci. 6, 1047-56.
64. Bright Wilson, E. (1990) An Introduction to Scientific Research. Dover, New York, pp. 191-3.
65. Brockhauser, S., Di Michiel, M., McGeehan, J. E., McCarthy, A. A. and Ravelli, R. B. G. (2008) X-ray tomographic reconstruction of macromolecular samples. J. Appl. Crystallogr. 41, 1057-66.
66. Buerger, M. J. (1940) The correction of X-ray diffraction intensities for Lorentz and polarization factors. Proc. Natl. Acad. Sci. USA 26, 637-42.
67. Burmeister, W. P. (2000) Structural changes in a cryo-cooled protein crystal owing to radiation damage. Acta Crystallogr. D 56, 328-41.
68. CCP4 (Collaborative Computational Project Number 4) (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760-3.
69. Corbett, M. C., Latimer, M. J., Poulos, T. L., Sevrioukova, I. F., Hodgson, K. O. and Hedman, B. (2007) Photoreduction of the active site of the metalloprotein putidaredoxin by synchrotron radiation. Acta Crystallogr. D 63., 951-60.
70. Dauter, Z. (2003) Twinned crystals and anomalous phasing.Acta Crystallogr. D 59, 2004-16.
71. Diamond, R. (1969) Profile analysis in single-crystal diffractometry. Acta Crystallogr. A 25, 43-54.
72. Evans, P. (2006) Scaling and assessment of data quality. Acta Crystallogr. D 62, 72-82
73. French, S. and Wilson, K. (1978) On the treatment of negative intensity observations. Acta Crystallogr. A 34, 517-25.
74. Garman, E. (1999) Cool data: quantity and quality. Acta Crystallogr. D 55, 1641-53.
75. Helliwell, J. R. (1992) Macromolecular Crystallography with Synchrotron Radiation. Cambridge University Press, Cambridge.
76. Huelson, G., Broennimann, C., Eikenberry, E. F. and Wagner, A. (2006) Protein crystallography with a novel large-area pixel detector. J. Appl. Crystallogr 39, 550-7.
77. Jeffrey, J. W. (1971) Methods in X-ray Crystallography. Academic Press, London and New York.
78. Kabsch, W. (1988a) Automatic indexing of rotation diffraction patterns. J. Appl. Crystallogr. 21, 67-71.
79. Kabsch, W. (1988b) Evaluation of single-crystal X-ray diffraction data from a positionsensitive detector. J. Appl. Crystallogr. 21, 916-24.
80. Kabsch, W. (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26, 795-800.
81. Kantardjieff, K. A. and Rupp, B. (2003) Matthews coefficient probabilities: improved estimates for unit cell contents of proteins, DNA and protein-nucleic-acid complex crystals. Protein Sci. 12, 1865-71.
82. Kittel, C. (2004) An Introduction to Solid State Physics, 8th edn. Wiley, New York.
83. Kusz, J. and Bohm, H. (2002) Performance of a confocal multilayer X-ray optic. J. Appl. Crystallogr. 35, 8-12.
84. Leslie, A. G. W. (2006) The integration of macromolecular diffraction data. Acta Crystallogr. D 62, 48-57.
85. Leslie, A. G. W., Powell, H. R., Winter, G., Svensson, O., Spruce, D., McSweeney, S., Love, D., Kinder, S., Duke, E. and Nave, C. (2002) Automation of the collection and processing of X-ray diffraction data-a generic approach. Acta Crystallogr. D 58, 1924-8.
86. Matthews, B. W. (1968) Solvent content of protein crystals. J. Molec. Biol. 33, 491-7.
87. Milch, J. R. and Minor, T. C. (1974) The indexing of single-crystal X-ray rotation photographs. J. Appl. Crystallogr. 7, 502-505.
88. North, A. C. T., Phillips, D. C. and Matthews, F. S. (1968) A semi-empirical method of absorption correction. Acta. Crystallogr. A 24, 351-9.
89. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data. Methods Enzymol. 276, 307-26.
90. Parsons, S. (2004) Introduction to twinning. Acta Crystallogr. D 59, 1995-2003.
91. Pflugrath, J. W. (1999) The finer things in X-ray diffraction. Acta Crystallogr. D 55, 1718-25.
92. Phillips, W. C. and Rayment, I. (1985) A systematic method for aligning double-focussing mirrors. Methods Enzymol. 114, 316-29.
93. Powell, H. R. (1999) The Rossmann Fourier autoindexing algorithm in MOSFLM. Acta Crystallogr. D 55, 1690-5.
94. Ravelli, R. B. G. and McSweeney, S. M. (2000) The fingerprint that X-rays leave on structures. Structure 8, 315-28.
95. Rossmann, M. G. (1979) Processing oscillation diffraction data for very large unit cells with an automatic convolution technique and profile fitting. J. Appl. Crystallogr. 12, 225-38.
96. Sanderson, M. R. (2007) In-house macromolecular data collection. In Macromolecular Crystallography, ed. Sanderson, M. and Skelly, J. V. Oxford University Press, Oxford, pp. 77-86.
97. Schwager, P., Bartels, K. and Huber, R. (1973) A simple empirical absorption-correction method for X-ray intensity data films. Acta Crystallogr. A 29, 291-5.
98. Stellar, I., Bolotovsky, R. and Harrison, S. C. (1997) An algorithm for automatic indexing of oscillation images using Fourier analysis. J. Appl. Crystallogr. 30, 1036-40.
99. Westbrook, E. M. and Naday, I. (1997) Charge-coupled device-based area detectors. Methods Enzymol. 276, 244-68.
100. Wilson, A. J. C. (1942) Determination of absolute from relative X-ray intensity data. Nature 150, 152.
101. Wilson, K. and Yeates, D. (1979) On the treatment of data measured on the oscillation camera. Acta Crystallogr. A 35, 146-57.
102. Wood, K., Frolich, A., Paciaroni, A., Moulin, M., Hartlein, M., Zaccai, G., Tobias, D. J. and Weik, M. (2008) Coincidence of dynamical transitions in a soluble protein and its hydration water: direct measurements by neutron scattering and MD simulations. J. Am. Chem. Soc. 130, 4585-7.
103. Yeates, T. O. and Fam, B. C. (1999) Protein crystals and their evil twins. Structure 7, 25-9.
104. Carter, C. W., Jr and Carter C. W. (1979) Protein crystallization using incomplete factorial experiments. J. Biol. Chem. 254, 12219-23.
105. Chayen, N. E. (1997) A novel technique to control the rate of vapour diffusion, giving larger protein crystals. J. Appl. Crystallogr. 30, 198-202.
106. Garman, E. F. and Doublie, S. (2003) Cryocooling of macromolecular crystals: optimisation methods. Methods Enzymol. 368, 188-216.
107. Jancarik, J. and Kim, S.-H. (1991) Sparse matrix sampling: a screening method for crystallization of proteins. J. Appl. Crystallogr. 24, 409-11.
108. Kundrot, C. E., Judge, R. A., Pusey, M. L. and Snell, E. H. (2001) Microgravity and macromolecular crystallography. Crystal Growth and Design 1, 87-99.
109. McPherson, A. (2004) Introduction to protein crystallization. Methods 34, 254-65.
110. Owens, R. J., Nettleship, J. E., Berrow, N. S., Sainsbury, S., Aricescu, R., Stuart, D. I. and Stammers, D. K. (2007) High-throughput cloning, expression and purification. In Macromolecular Crystallography, ed. Sanderson, M. and Skelly, J. V. Oxford University Press, Oxford, pp. 23-41.
111. Skelly, J., Sohi, M. K. and Batuwangala, T. (2007) Classical cloning, expression and purification. In Macromolecular Crystallography, ed. Sanderson, M. and Skelly, J. V. Oxford University Press, Oxford, pp. 1-22.
112. Bracewell, R. M. The Fourier Transform and Its Applications, 3rd edn. McGraw-Hill, New York, 1999.
113. Papoulis, A. The Fourier Integral and its Applications. McGraw-Hill, New York, 1962.
114. Braddick, H. J. J. Vibrations, Waves and Diffraction. McGraw-Hill, London, 1965.
115. Lipson, H. and Taylor, C. A. Fourier Transforms and X-ray Diffraction. Bell, London, 1958.
116. Stuart, R. D. An Introduction to Fourier Analysis. Methuen, London, 1966.
117. Blow, D. Outline of Crystallography for Biologists. Oxford University Press, Oxford, 2002.
118. Rhodes, G. Crystallography Made Crystal Clear: A Guide for Users of Macromolecular Models, 3rd edn. Academic Press, Burlington, MA, 2006.
119. Blundell, T. L. and Johnson, L. N. Protein Crystallography. Academic Press, New York, 1976.
120. Cantor, C. R. and Schimmel, P. R. Biophysical Chemistry, Part II: Techniques for the Study of Biological Structure and Function. Freeman, San Francisco, 1980.
121. Drenth, J. Principles of Protein X-ray Crystallography, 3rd edn. Springer, New York, 2007.
122. Giacovazzo, C., Monaco, H. L., Artioli, G., Viterbo, D., Ferraris, G., Gilli, G., Zanotti, G. and Catti, M. Fundamentals of Crystallography, 2nd edn, International Union of Crystallography Texts on Crystallography. Oxford University Press, Oxford, 2002.
123. Helliwell, J. R. Macromolecular Crystallography with Synchrotron Radiation. Cambridge University Press, Cambridge, 1992.
124. Ladd, M. F. C. and Palmer, R. A. Structure Determination by X-ray Crystallography, 4th edn. Plenum, New York, 2003.
125. Messerschmidt, A. X-Ray Crystallography of Biomacromolecules: A Practical Guide. Wiley, Weinheim, 2007.
126. Sanderson, M. R. and Skelly, J. V. Macromolecular Crystallography: Conventional and High-Throughput Methods. Oxford University Press, Oxford, 2007.
127. Stout, G. H. and Jensen, L. H. X-ray Structure Determination: A Practical Guide, 2nd edn. Wiley, New York, 1989.
128. Woolfson, M. M. An Introduction to X-ray Crystallography, 2nd edn. Cambridge University Press, Cambridge, 1997.
129. International Tables for Crystallography, Volumes A-G. International Union of Crystallography, Chester, UK, 2006.
130. Brünger, A. T. (1990) Extension of molecular replacement: a new search strategy based on Patterson correlation refinement. Acta Crystallogr. A 46, 46-57.
131. Crowther, R. A. (1972) The fast rotation function. In The Molecular Replacement Method, ed. Rossmann, M. G. Gordon & Breach, New York, pp. 173-8.
132. Crowther, R. A. and Blow, D. M. (1967) A method of positioning a known molecule in an unknown crystal structure. Acta Crystallogr. 23, 544-8.
133. Dodson, E. (2008) The befores and afters of molecular replacement. Acta Crystallogr. D 64, 17-24.
134. Driessen, H. P. C., Bax, B., Slingsby, C., Lindley, P. F., Mahadevan, D., Moss, D. S. and Tickle, I. J. (1991) Structure of oligomeric β-B2-crystallin-an application of the T 2 translation function to an asymmetric unit containing 2 dimers. Acta Crystallogr. B 47, 987-97.
135. Evans, P. R. (2001) Rotations and rotation matrices. Acta Crystallogr. D 57, 1355-9.
136. Grosse-Kunstleve, R. W. and Adams, P. D. (2001) Patterson correlation methods: a review of molecular replacement with CNS. Acta Crystallogr. D 57, 1390-6.
137. Harada, Y., Lifchitz, A., Berthou, J. and Jolles, P. (1981) A translation function combining packing and diffraction information: an application to lysozyme (high-temperature form). Acta Crystallogr. A 37, 398-406.
138. Hirshfeld, F. L. (1968) Symmetry in the generation of trial structures. Acta Crystallogr. A 24, 301-11.
139. Huber, R. (1965) Die automatisierte faltemolekulemethode. Acta Crystallogr. 19, 353-6.
140. Kissinger, C. R., Gehlhaar, D. K. and Fogel, D. B. (1999) Rapid automated molecular replacement by evolutionary search. Acta Crystallogr. D 55, 484-91.
141. Kissinger, C. R., Gelhaar, D. K., Smith, B. A. and Bouzida, D. (2001) Molecular replacement by evolutionary search. Acta Crystallogr. D 57, 1474-9.
142. Lattman, E. E. (1972) Optimal sampling of the rotation function. Acta Crystallogr. B 28, 1065-8.
143. Lattman, E. E. and Love W. E. (1970) A rotational search procedure for detecting a known molecule in a crystal. Acta Crystallogr. B 26, 1854-7.
144. Lattman, E. E. and Love, W. E. (1971) Acta Crystallogr. B 27, 1479.
145. Lebedev, A. A., Vagin, A. A. and Murshudov, G. N. (2008) Model preparation in MOLREP and examples of model improvement using X-ray data.Acta Crystallogr. D 64, 33-9.
146. McCoy, A. J. (2007) Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr. D 63, 32-41.
147. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C. and Read, R. J. (2005) Likelihoodenhanced fast translation functions. Acta Crystallogr. D 61, 458-64.
148. Moss, D. S. (1985) The symmetry of the rotation function. Acta Crystallogr. A 41, 470-5.
149. Navaza, J. (1994) AMoRe: an automated package for molecular replacement. Acta Crystallogr. A 50, 157-63.
150. Navaza, J. (2001) Implementation of molecular replacement in AMoRe. Acta Crystal-logr. D 57, 1367-72.
151. Navaza, J. (2008) Combining X-ray and electron-microscopy data to solve crystal structures. Acta Crystallogr. D 64, 70-5.
152. Read, R. J. (2001) Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr. D 57, 1373-82.
153. Rossmann, M. G. and Blow, D. M. (1962) The detection of subunits within the crystallographic asymmetric unit. Acta Crystallogr. 15, 24-31.
154. Tollin, P. and Rossmann, M. G. (1966) A description of various rotation function programs. Acta Crystallogr. 21, 872-6.
155. Storoni, L. C., McCoy, A. J. and Read, R. J. (2004) Likelihood-enhanced fast rotation functions. Acta Crystallogr. D 60, 432-8.
156. Tickle, I. J. and Driessen, H. P. C. (1995) Molecular replacement using known structural information. In Crystallographic Methods and Protocols, ed. Jones, C., Mulloy, B. and Sanderson, M. R., Methods in Molecular Biology, Volume 56, pp. 173-203.
157. Trapani, S. and Navaza, J. (2008) AMoRe: classical and modern. Acta Crystallogr. D 64, 11-6.
158. Vagin, A. and Teplyakov, A. (1997) MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30, 1022-5.
159. Xiong, Y. (2008) From electron microscopy to X-ray crystallography: molecularreplacement case studies. Acta Crystallogr. D 64, 76-82.
160. Agarwal, R. C. (1978) A new least-squares refinement technique based on the fast Fourier transform algorithm. Acta Crystallogr. A 34, 791-809.
161. Badger, J. (2003) An evaluation of automated model-building procedures for protein crystallography. Acta Crystallogr. D 59, 823-7.
162. Blow, D. M. and Crick, F. H. C. (1959) The treatment of errors in the isomorphous replacement method. Acta Crystallogr. 12, 794-802.
163. Booth, A. D. (1949) The refinement of atomic parameters by the technique known in X-ray crystallography as 'the method of steepest descents'. Proc. Roy. Soc. A 197, 336-55.
164. Brönger, A. T. (1997) Free R value: cross-validation in crystallography. Methods Enzymol. 277, 366-96.
165. Brönger, A. T. and Rice, L. M. (1997) Crystallographic refinement by simulated annealing: methods and applications. Methods Enzymol. 277, 243-69.
166. Brönger, A. T., Kuriyan, J. and Karplus, M. (1987) Crystallographic R factor refinement by molecular dynamics. Science 235, 458-60.
167. Brönger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, N., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography and NMR system (CNS): A new software system for macromolecular structure determination. Acta Crystallogr. D 54, 905-21.
168. Coates, L., Erskine, P. T., Crump, M. P., Wood, S. P. and Cooper, J. B. (2001) Five atomic resolution structures of endothiapepsin inhibitor complexes: implications for the aspartic proteinase mechanism. J. Molec. Biol. 318, 1405-15.
169. Diamond, R. (1971) A real-space refinement procedure for proteins. Acta Crystallogr. A 27, 436-52.
170. Emsley, P. and Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-32.
171. Engh, R. A. and Huber, R. (1991) Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A 47, 392-400.
172. Farrugia, L. J. (1997) Ortep-3 for Windows. J. Appl. Crystallogr. 30, 565.
173. Fletterick, R. J. and Wyckoff, H. W. (1975) Preliminary refinement of protein coordinates in real space. Acta Crystallogr. A 31, 698-700.
174. Fisher, S. J., Helliwell, J. R., Khurshid, S., Govada, L., Redwood, C., Squire, J. M. and Chayen, N. E. (2008) An investigation into the protonation states of the C1 domain of cardiac myosin-binding protein C. Acta Crystallogr. D 64, 658-64.
175. Greer, J. (1974) Three-dimensional pattern recognition: an approach to automated interpretation of electron density maps of proteins. J. Molec. Biol. 82, 279-301.
176. Haneef, I., Moss, D. S., Stanford M. J. and Borkakoti, N. (1985) Restrained structure-factor leastsquares refinement of protein structures using a vector processing computer. Acta Crystallogr. A 41, 426-33.
177. Hendrickson, W. A. and Konnert, J. H. (1980) Incorporation of stereochemical information into crystallographic refinement. In Computing in Crystallography, ed. Diamond, R. Indian Institute of Science, Bangalore, India, Chapter 13, pp. 1-23.
178. claHolm, L. and Sander, C. (1995) Dali: a network tool for protein structure comparison. Trends Biochem. Sci. 20, 478-80.
179. Hughes, E. W. (1941) The crystal structure of melamine. J. Am. Chem. Soc. 63, 1737-52.
180. Hughes, E. W. (1978) The crystal structure of melamine. Current Contents 40, 13-13.
181. Ioerger, T. R. and Sacchettini, J. C. (2002) Automatic modeling of protein backbones in electron density maps via prediction of Cα coordinates. Acta Crystallogr. D 58, 2043-54.
182. Jack, A. and Levitt, M. (1978) Refinement of large structures by simultaneous minimization of energy and R factor. Acta Crystallogr. A 34, 931-5.
183. Jones, T. A. (1978) A graphics model building and refinement system for macromole-cules. J. Appl. Crystallogr. 11, 268-72.
184. Lamzin, V., Morris, R. and Perrakis, A. (2001) Automatic building and refinement of protein crystal structures. In Advances in Structure Analysis, ed. Kuzel, R. and Hasek, J. Czech & Slovak Crystallographic Association, Prague, pp. 73-80.
185. Laskowski, R. A., MacArthur, M. W., Moss, D. S. and Thornton, J. M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-91.
186. Levitt, D. G. (2001) A new software routine that automates the fitting of protein X-ray crystallographic electron-density maps. Acta Crystallogr. D 57, 1013-9.
187. Lovell, S. C., Davis, I. W., Arendall, B., de Bakker, P. I. W., Word, J. M., Prisant, M. G., Richardson, J. S. and Richardson, D. C. (2003) Structure validation by Cα geometry: Φ, ψ, and Cβ deviation. Proteins Struct. Funct. Genet. 50, 437-50.
188. Luzzati, V. (1952) Traitement statistique des erreurs dans la determination des structures cristallines. Acta Crystallogr. 5, 802-10.
189. Main, P. (1979) A theoretical comparison of the β, γ' and 2 F °-F c syntheses. Acta Crystallogr. A 35, 779-85.
190. Moews, P. C. and Kretsinger, R. H. (1975) Refinement of the structure of carp muscle calciumbinding parvalbumin by model building and difference Fourier analysis. J. Molec. Biol. 91, 201-25.
191. Murshudov, G. N., Vagin, A. A. and Dodson, E. J. (1997) Refinement of macro-molecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240-55.
192. Oldfield, T. J. (2003) Automated tracing of electron-density maps of proteins. Acta Crystallogr. D 59, 483-91.
193. Perrakis, A., Sixma, T. K., Wilson, K. S. and Lamzin, V. S. (1997) wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atom models. Acta Crystallogr. D 53, 448-55.
194. Read, R. J. (1986) Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A 42, 140-9.
195. Ruiz, F., Hazemann, I., Mitschler, A., Joachimiak, A., Schneider, T. R., Karplus, M. and Podjarny, A. D. (2005) The crystallographic structure of aldose reductase-IDD552 complex shows direct proton donation from tyrosine 48. Acta Crystallogr. D 60, 1347-54.
196. Schuettelkopf, A. W. and van Aalten, D. M. F. (2004) PRODRG-a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D 60, 1355-63.
197. Schomaker, V. and Trueblood, K. N. (1968) On the rigid-body motion of molecules in crystals. Acta Crystallogr. B 24, 63-76.
198. Sheldrick, G. M. and Schneider, T. R. (1997) SHELXL: high-resolution refinement. Methods Enzymol. 277, 319-43.
199. Sim, G. A. (1959) The distribution of phase angles for structures containing heavy atoms. II. A modification of the normal heavy-atom method for non-centrosymmetrical structures. Acta Crystallogr. 12, 813-5.
200. Sim, G. A. (1960) A note on the heavy-atom method. Acta Crystallogr. 13, 511-2.
201. Srinivasan, R. and Ramachandran, G. N. (1965) Probability distribution connected with structure amplitudes of two related crystals. V. The effect of errors in the atomic coordinates on the distribution of observed and calculated structure factors. Acta Crystallogr. 19, 1008-14.
202. Sussmann, J. L., Holbrook, S. R., Church, G. M. and Kim, S.-H. (1977) A structure-factor leastsquares refinement procedure for macromolecular structures using constrained and restrained parameters. Acta Crystallogr. A 33, 800-804.
203. Ten Eyck, L. F. (1977) Efficient structure-factor calculation for large molecules by the fast Fourier transform. Acta Crystallogr. A 33, 486-92.
204. Terwilliger, T. C. (2003a) Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr. D 59, 38-44.
205. Terwilliger, T. C. (2003b) Automated side-chain model building and sequence assignment by template-matching. Acta Crystallogr. D 59, 45-9.
206. Tickle, I. J., Laskowski, R. A. and Moss, D. S. (1998) R free and the R free ratio. I. Derivation of expected values of cross-validation residuals used in macromolecular least squares refinement. Acta Crystallogr. D 54, 547-57.
207. Tickle, I. J., Laskowski, R. A. and Moss, D. S. (2000) R free and the R free ratio. II. Calculation of the expected values and variances of cross-validation statistics in macromolecular least-squares refinement. Acta Crystallogr. D 56, 442-50.
208. Tronrud, D. E. (2004) Introduction to macromolecular refinement. Acta Crystallogr. D 60, 2156-68.
209. Tronrud, D. E., Ten Eyck, L. F. and Matthews, B. W. (1987) An efficient generalpurpose least squares refinement program for macromolecular structures. Acta Crystallogr. A 43, 489-501.
210. Verlet, L. (1967) Computer 'experiments' on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159, 98-103.
211. Waser, J. (1963) Least-squares refinement with subsidiary conditions. Acta Crystal-logr. A 16, 1091-4.
212. Wilson, A. J. C. (1942) Determination of absolute from relative X-ray intensity data. Nature (Lond.) 150, 151-2.
213. Winn, M. D., Isupov, M. N. and Murshudov, G. N. (2001) Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D 57, 122-33.
214. Abdel-Meguid, S. S. (1995) Structure determination using isomorphous replacement. In Crystallographic Methods and Protocols, ed. Jones, C., Mulloy, B. and Sanderson, M. R., Methods in Molecular Biology, Volume 56, 153-71.
215. Abrahams, J. P. and Leslie, A. G. W. (1996) Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallogr. D 52, 30-42.
216. Blessing, R. H. (1997) LOCSCL: a program to statistically optimize local scaling of singleisomorphous replacement and single-wavelength-anomalous-scattering data. J. Appl. Crystallogr. 30, 176-7.
217. Blessing, R. H. and Smith, G. D. (1999) Difference structure-factor normalisation for heavy-atom or anomalous scattering substructure determinations. Acta Crystallogr. 32, 664-70.
218. Bloomer, A. (1983) Peaks and holes at heavy atom sites. Daresbury Laboratory, UK. Info. Q. Protein Crystallogr. 11, 41-6
219. Blow, D. M. and Crick, F. H. C. (1959) The treatment of errors in the isomorphous replacement method. Acta Crystallogr. 12, 794-802.
220. Blow, D. M. and Rossmann, M. G. (1961) The single isomorphous replacement method. Acta Crystallogr. 14, 1195-1202.
221. Blundell, T. L. and Johnson, L. N. (1976) Protein Crystallography. Academic Press, New York.
222. Boggon, T. J. and Shapiro, L. (2000) Screening for phasing atoms in protein crystallography. Structure 8, 143-9.
223. CCP4 (Collaborative Computational Project Number 4) (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760-3.
224. Coster, D. (1924) Uber die absorptionsspektren im Rontgengebiet. Z. Phys. 25, 83-98.
225. Cowtan, K. (1994) DM: an automated procedure for phase improvement by density modification. Joint CCP4 ESF-EACBM Newslett. Protein Crystallogr. 31, 34-8.
226. Cullis, A. F., Muirhead, H., Perutz. M. F., Rossmann, M. G. and North, A. C. T. (1961) The structure of haemoglobin. VIII. A three-dimensional Fourier synthesis at 5.5 Å resolution:determination of the phase angles. Proc. Roy. Soc. A 265, 15-38.
227. Dauter, Z. (2002) New approaches to high-throughput phasing. Curr. Opin. Struct. Biol. 12, 674-8.
228. De la Fortelle, E. and Bricogne, G. (1997) Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472-94.
229. Dodson, E. (2003) Is it jolly SAD? Acta Crystallogr. D 59, 1958-65.
230. Dodson, E. and Vijayan, M. (1971) The determination and refinement of heavy-atom parameters in protein heavy-atom derivatives. Some model calculations using acentric reflections. Acta Crystallogr. B 27, 2402-11.
231. Drenth, J. (2007) Principles of Protein X-ray Crystallography, 3rd edn. Springer, New York.
232. Ealick, S. E. (1997) Now we're cooking: new successes for shake-and-bake. Structure 5, 469-72.
233. Evans, G. and Pettifer, R. F. (2001) CHOOCH: a program for deriving anomalousscattering factors from X-ray fluorescence spectra. J. Appl. Crystallogr. 34, 82-6.
234. Frazão, C., Soares, C. M., Carrondo, M. A., Pohl, E., Dauter, Z., Wilson, K. S., Hervés, M., Navarro, J. A., De la Rosa, M. A. and Sheldrick, G. M. (1995) Ab initio determination of the crystal structure of cytochrome c 6 and comparison with plastocyanin. Structure 3, 1159-69.
235. Germain, G., Main, P. and Woolfson, M. M. (1970) On the application of phase relationships to complex structures. II. Getting a good start. Acta Crystallogr. B 26, 274-85.
236. González, A. (2003) Optimising data collection for structure determination. Acta Crystallogr. D 59, 1935-42.
237. Grosse-Kunstleve, R. W. and Adams, P. D. (2003) On the symmetries of substructures. Acta Crystallogr. D 59, 1974-7.
238. Hai-Fu, F., Woolfson, M. M. and Jia-Xing, Y. (1993) New techniques of applying multiwavelength anomalous scattering data. Proc. Roy. Soc. Lond. A 442, 13-32.
239. Hao, Q., Gu, Y. X., Zheng, C. D. and Fan, H. F. (2000) OASIS: a computer program for breaking phase ambiguity in one-wavelength anomalous scattering or single isomorphous substitution (replacement) data. J. Appl. Crystallogr. 33, 980-1.
240. Helliwell, J. R. (1992) Macromolecular Crystallography with Synchrotron Radiation. Cambridge University Press, Cambridge.
241. Hendrickson, W. A. (1991) Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science, 254, 51-8.
242. Hendrickson, W. A. and Lattman, E. E. (1970) Representation of the phase probability distributions for simplified combination of independent phase information. Acta Crystallogr. B 26, 136-43.
243. Howell, P. L. and Smith, G. D. (1992) Identification of heavy-atom derivatives by normal probability methods. J. Appl. Crystallogr. 25, 81-6.
244. Karle, J. and Hauptman, H. (1956) A theory of phase determination for the four types of non-centrosymmetric space groups. Acta Crystallogr. 9, 635-51.
245. Kartha, G. (1975) Applications of anomalous scattering studies in protein structure analysis. In Anomalous Scattering, ed. Ramaseshan, S. and Abrahams, S. C. Munks-gaard, Copenhagen, pp. 363-91.
246. Kleywegt, G. J. and Jones, T. A. (1994) Halloween... masks and bones. In From First Map to Final Model, ed. Bailey, S., Hubbard, R. and Waller, D. Daresbury Laboratory, Warrington, UK, pp. 59-66.
247. Kraut, J., Sieker, L., High, D. F. and Freer, S. T. (1962) Chymotrypsinogen: a three dimensional Fourier synthesis at 5 Å resolution. Proc. Natl. Acad. Sci. USA 48, 1417-24.
248. Ladd, M. F. C. and Palmer, R. A. (2003) Structure Determination by X-ray Crystallography, 4th edn. Springer, New York.
249. Leslie, A. G. W. (1987) A reciprocal-space method for calculating a molecular envelope using the algorithm of B.C. Wang. Acta Crystallogr A 43, 134-6.
250. Leslie, A. (1991) Heavy atom derivative screening. In Isomorphous replacement and anomalous scattering, ed. Wolf, W., Evans, P. R. and Leslie, A. G. W. Daresbury Laboratory, Warrington, UK, pp. 9-22.
251. Lu, G. (1999) FINDNCS: a program to detect non-crystallographic symmetries in protein crystals from heavy atoms sites. J. Appl. Crystallogr. 32, 365-8.
252. Matthews, B. W. (1966) The extension of the isomorphous replacement method to include anomalous scattering measurements. Acta Crystallogr. 20, 82-6.
253. Matthews, B. W. and Czerwinski, E. W. (1975) Local scaling: a method to reduce systematic errors in isomorphous replacement and anomalous scattering measurements. Acta Crystallogr. A 31, 480-7.
254. Petsko, G. A. (1985) Preparation of isomorphous heavy-atom derivatives. Methods Enzymol. 114, 147-57.
255. Phillips, J. C. and Hodgson, K. O. (1980) The use of anomalous scattering effects to phase diffraction patterns from macromolecules. Acta Crystallogr. A 36, 856-64.
256. Read, R. J. (1986) Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A 42, 140-9.
257. Sauer, O., Schmidt, A. and Kratky, C. (1997) Freeze-trapping isomorphous xenon derivatives of protein crystals. J. Appl. Crystallogr. 30, 476-86.
258. Sayre, D. (1952) The squaring method: a new method for phase determination. Acta Crystallogr. 5, 60-5.
259. Schneider, T. R. and Sheldrick, G. M. (2002) Substructure solution with SHELXD. Acta Crystallogr. D 58, 1772-9.
260. Sheldrick, G. M. (2008) A short history of SHELX. Acta Crystallogr. 64, 112-22.
261. Sheldrick, G. M., Dauter, Z., Wilson, K. S., Hope, H. and Sieker, L. C. (1993) The application of direct methods and Patterson interpretation to high-resolution native protein data. Acta Crystallogr. D 49, 18-23.
262. Singh, A. K. and Ramaseshan, S. (1966) The determination of heavy atom positions in protein derivatives. Acta Crystallogr. 21, 279.
263. Terwilliger, T. C. (1994a) MAD phasing: Bayesian estimates of F A. Acta Crystallogr. D 50, 11-6.
264. Terwilliger, T. C. (1994b) MAD phasing: treatment of dispersive differences as isomorphous replacement information. Acta Crystallogr. D 50, 17-23.
265. Terwilliger, T. C. (2000) Maximum likelihood density modification. Acta Crystallogr. D 56, 965-72.
266. Terwilliger, T. C. (2002a) Statistical density modification with non-crystallographic symmetry. Acta Crystallogr D. 58, 2082-6.
267. Terwilliger, T. C. (2002b) Rapid automatic NCS identification using heavy-atom substructures. Acta Crystallogr. D 58, 2213-5.
268. Terwilliger, T. C. and Berendzen, J. (1999a) Automated MAD and MIR structure solution. Acta Crystallogr. D 55, 849-61.
269. Terwilliger, T. C. and Berendzen, J. (1999b) Discrimination of solvent from protein regions in native Fouriers as a means of evaluating heavy-atom solutions in the MIR and MAD methods. Acta Crystallogr. D 55, 501-505.
270. Terwilliger, T. C. and Eisenberg, D. (1983) Unbiased three-dimensional refinement of heavy-atom parameters by correlation of origin-removed Patterson functions. Acta Crystallogr. A 39, 813-7.
271. Terwilliger, T. C. and Eisenberg, D. (1987) Isomorphous replacement: effects of errors on the phase probability distribution. Acta Crystallogr. A 43, 6-13.
272. Terwilliger, T. C., Sung-Hou, K. and Eisenberg, D. (1987) Generalised method of determining heavy-atom positions using the difference Patterson function. Acta Crystallogr. A 43, 1-5.
273. Terwilliger, T. C., Grosse-Kunstleve, R. W., Afonine, P. V., Moriarty, N. W., Zwart, P. H., Hung, L.-W., Read, R. J. and Adams, P. D. (2008) Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr. D 64, 61-9.
274. Tickle, I. J. (1983) Local scaling of heavy-atom derivative data and the solution of heavyatom difference Pattersons by vector-search. Daresbury Laboratory, UK. Info. Q. Protein Crystallogr. 11, 5-10.
275. Tickle, I. J. (1991) Refinement of single isomorphous replacement heavy-atom parameters in Patterson versus reciprocal space. In Isomorphous Replacement and Anomalous Scattering, ed. Wolf, W., Evans, P. R. and Leslie, A. G. W. Daresbury Laboratory, Warrington, UK, pp. 87-95.
276. Tickle, I. J. (1992) LOCAL: local scaling program for heavy atom derivatives. Dares-bury laboratory, UK. Joint CCP4 ESF-EACM Newslett. Protein Crystallogr. 26, 22-6.
277. Wang, B. C. (1985) Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol. 115, 90-112.
278. Wang, J., Wlodawer, A. and Dauter, Z. (2007) What happens when the signs of the anomalous differences or the handedness of the substructure are inverted. Acta Crystallogr. D 63, 751-8.
279. Weeks, C. M. and Furey, W. (2007) Application of direct methods to macromolecular structure solution. In Macromolecular Crystallography: Conventional and High Throughput Methods-A Practical Approach, ed. Sanderson, M. and Skelly, J. Oxford University Press, Oxford, pp. 129-41.
280. Weeks, C. M., Sheldrick, G. M., Miller, R., Usón, I. and Hauptman, H. A. (2001) Ab initio phasing by dual-space direct methods. In Advances in Structure Analysis, ed. Kuzel, R. and Hasek, J. Czech & Slovak Crystallographic Association, Prague, pp. 37-64.
281. Woolfson, M. M. (1997) An Introduction to X-ray Crystallography. Cambridge University Press, Cambridge.
282. Xu, H. and Weeks, C. M. (2008) Rapid automated substructure solution by Shake-and-Bake. Acta Crystallogr. D 64, 172-7.
283. Yao, J. X., Dodson, E. J., Wilson, K. S. and Woolfson, M. M. (2006) ACORN: a review. Acta Crystallogr. D 62, 901-908.
284. Zhang, K. Y. J. and Main, P. (1990) Histogram matching as a new density modification technique for phase refinement and extension of protein molecules. Acta Crystallogr. A 46, 41-6.
285. Bozzola, J. and Russell, L. D. Electron Microscopy: Principles and Techniques for Biologists. Jones and Bartlett, Sudbury, MA, 1999.
286. Frank, J. Three-Dimensional Electron Microscopy of Macromolecular Assemblies:Visualization of Biological Molecules in Their Native State. Oxford University Press, Oxford, 2006.
287. Morris, V. J., Kirby, A. R. and Gunning, A. P. Atomic Force Microscopy for Biologists. Imperial College Press, London, 1999.
288. Buerger, M. J. Vector Space. Wiley, New York, 1959.
289. Jeffrey, A.Mathematics for Engineers and Scientists, 6th edn. CRC Press, Boca Raton,FL, 2005.
290. Stephenson, G.Mathematical Methods for Science Students. Longman, London, 1973.