Jack Tanner's Essential Reading List for Protein Crystallographers

(content is intended for internal use only and is therefore protected)

Introduction

• Historical background by Rossmann, International Tables F, p. 4-9
• Macromolecular crystallography and medicine, International Tables F, p. 10-25

Crystallization

• FIND ME®McPherson's classic review paper (McPherson 1990)
• Weber's short review (Weber 1997)
• FIND ME®Seeding (Stura and Wilson 1990)
• Incomplete factorial method (Carter and Carter 1979)
• Small-scale batch method (Rayment 2002)
• Bergfors' Crystallization Lab Manual (http://web.missouri.edu/~brd475/manual.html)
• Dynamic light scattering as indicator of crystallizability (Ferre-D'Amare and Burley 1997)
• FIND ME®Aggregation and crystallization (Zulauf and D'Arcy 1992)

Basic principles of X-ray diffraction

• “Branden and Tooze Chapter 18: Determination of Protein Structures” (Brändén and Tooze 1999)
• “Tinoco, Sauer, Wang, and Puglisi Chapter 12: Macromolecular Structure and X-ray Diffraction” (Tinoco et al. 2002)
• "Basic Crystallography" by J. Drenth, International Tables F, p. 45-63
• “Stout and Jensen Chapter 1: X-rays”; “Stout and Jensen Chapter 2: Diffraction of X-rays” (Stout and Jensen 1989)

Symmetry in crystallography

• “Stout and Jensen Chapter 3: Crystals, Symmetry, and Space Groups” (Stout and Jensen 1989)

• "Basic Crystallography" by J. Drenth, International Tables F, p. 45-63

Preparing crystals for data collection

• Preparing crystals for cryogenic data collection (Rodgers 1994)
• Practical cryocrystallography also by Rodgers (Rodgers 1997)
• Cross-linking crystals with glutaraldehyde (Lusty 1999)

X-ray diffraction data collection

• Z. Dauter, "Data Collection Strategy"(Dauter 1997)
• Principles of monochromatic data collection, Dauter and Wilson, Int. Tables F, p. 177-195
• “Stout and Jensen Chapter 6: Intensity Data Collection” (Stout and Jensen 1989)

Processing of X-ray diffraction data

• “Stout and Jensen Chapter 7: Data Reduction” (Stout and Jensen 1989)
• Indexing (unit cell determination) by Rossmann, International Tables F, p. 209-211
• Integration by Leslie, International Tables F, 212-217
• Processing using the HKL suite by Otwinowski, International Tables F, p. 226-235

Structure Factors and Fourier Synthesis

• "Basic Crystallography" by J. Drenth, International Tables F, p. 45-63

• “Stout and Jensen Chapter 8: Theory of structure factors and Fourier syntheses” (Stout and Jensen 1989)
• “Stout and Jensen Chapter 9: Calculation of structure factors and Fourier syntheses” (Stout and Jensen 1989)

The phase problem

• Introduction to the phase problem (Taylor 2003)

Molecular replacement

• Rotations and rotation matrices (Evans 2001).
• Molecular replacement using AMoRe (Navaza 2001).
• Molecular replacement with CNS (Grosse-Kunstleve and Adams 2001).

Multiple isomorphous replacement (MIR) - preparation of derivatives

• Preparation of derivatives, International Tables F, p. 247-255
• More on preparation of derivatives, (Garman and Murray 2003).
• Screening for heavy atom derivatives (Rould 1997)
• Quick-soaking methods (Sun et al. 2002).
• Trimethyllead acetate (Holden and Rayment 1991).

Multiple isomorphous replacement (MIR) - theory

• Locating heavy-atom sites, International Tables F, p. 256-262
• FIND ME®W. Furey, Jr., ACA 1994 Workshop on Isomorphous Replacement Methods in Macromolecular Crystallography, p. 1-15.
• Overview of MIR phasing (Ke 1997)

Multiwavelength anomalous dispersion (MAD)

• Introduction to MAD by Smith and Hendrickson, International Tables F, p. 299-303
• Hendrickson and Ogata review of MAD phasing, (Hendrickson and Ogata 1997).
• FIND ME®Hendrickson's review in Science, (Hendrickson 1991)
• Preparation of Se-Met protein (Doublie 1997)
• Automated MAD/MIR structure determination by SOLVE, International Tables F, p. 303-307
• Halide soaking 2000 and 2001 (Dauter et al. 2000; Dauter et al. 2001)
• Optimizing data MAD data collection (Gonzalez 2003)

Single-wavelength anomalous diffraction (SAD)

• Jolly SAD review (Dauter et al. 2002)

• Heavy-atom location and phasing from single wavelength data by Matthews, International Tables F, p. 293-298.

• In house S-SAD phasing 2003a and 2003b by Sheldrick (Debreczeni et al. 2003a; Debreczeni et al. 2003b)
• In-house S-SAD phasing (Yang and Pflugrath 2001)
• S-SAD phasing in molecular replacement (Schuermann and Tanner 2003)

Twinning

• Moody's introduction to twinning (Chandra et al. 1999)
• Minireview: Protein crystals and their evil twins (Yeates and Fam 1999)
• Another introduction to twinning (Parsons 2003)
• Classic Rees papers on twinning 1980 and 1982 (Rees 1980; 1982)
• Bacteriorhodopsin perfect merohedral twinning (Luecke et al. 1998)
• Lactoferrin merohedral twinning (Breyer et al. 1999)
• Plastocyanin perfect hemihedral twinning (Redinbo and Yeates 1993)
• Perfect hemihedral twinning (Contreras-Martel et al. 2001)

Refinement

• Introduction to refinement, International Tables F, p. 369
• Engh and Huber geometry restraints, International Tables F, p. 382.
• Simulated annealing refinement, International Tables F, p. 375.
• CNS (Brünger et al. 1998)
• More on CNS, International Tables F, p. 710.

R-factor and Rfree

• FIND ME®Lattman's paper asking why protein R-factors are so high (Lattman 1996)
• Petsko's paper asking why protein R-factors are so high (Vitkup et al. 2002)
• Brunger's original cross validation (Rfree) papers in (FIND ME®1992) and 1993 (Brünger 1992; Brünger 1993)
• Application of Rfree (Kleywegt and Brünger 1996)

Coordinate uncertainty

• Introduction to coordinate uncertainty by Cruickshank, International Tables F, p. 403.
• Luzzati's original paper (in French) (Luzzati 1952)
• SigmaA (Read 1986)

Model Building and Validation

• Coot: model-building tools for molecular graphics by Paul Emsley (Emsley and Cowtan 2004) see also the user-manual
• Model building and refinement practice by Kleywegt and Jones, (Kleywegt and Jones 1997)
• O and RAVE packages, International Tables F, p. 353.
• Arp/Warp automated model building, International Tables F, p. 720.
• PROCHECK, International Tables F, p. 722

References

Brändén, C.-I., and Tooze, J. 1999. Introduction to protein structure, 2nd ed. Garland Pub., New York, pp. xiv, 410.

Breyer, W.A., Kingston, R.L., Anderson, B.F., and Baker, E.N. 1999. On the molecular-replacement problem in the presence of merohedral twinning: structure of the N-terminal half-molecule of human lactoferrin. In Acta Crystallogr., pp. 129-138.

Brünger, A.T. 1992. The Free R value: A novel statistical quantity for the assessing the accuracy of crystal structures. In Nature, pp. 472-474.

Brünger, A.T. 1993. Assessment of phase accuracy by cross validation: the free R value. Methods and applications. In Acta Crystallogr., pp. 24-36.

Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., et al. 1998. Crystallography & NMR system: A new software suite for macromolecular structure determination. In Acta Crystallogr., pp. 905-921.

Carter, C.W., Jr., and Carter, C.W. 1979. Protein crystallization using incomplete factorial experiments. In J. Biol. Chem., pp. 12219-12223.

Chandra, N., Acharya, K.R., and Moody, P.C. 1999. Analysis and characterization of data from twinned crystals. In Acta Crystallogr., pp. 1750-1758.

Contreras-Martel, C., Martinez-Oyanedel, J., Bunster, M., Legrand, P., Piras, C., Vernede, X., and Fontecilla-Camps, J.C. 2001. Crystallization and 2.2 A resolution structure of R-phycoerythrin from Gracilaria chilensis: a case of perfect hemihedral twinning. In Acta Crystallogr., pp. 52-60.

Dauter, Z. 1997. Data Collection Strategy. In Methods Enzymol., pp. 326-344.

Dauter, Z., Dauter, M., and Dodson, E. 2002. Jolly SAD. In Acta Crystallogr., pp. 494-506.

Dauter, Z., Dauter, M., and Rajashankar, K.R. 2000. Novel approach to phasing proteins: derivatization by short cryo-soaking with halides. In Acta Crystallogr., pp. 232-237.

Dauter, Z., Li, M., and Wlodawer, A. 2001. Practical experience with the use of halides for phasing macromolecular structures: a powerful tool for structural genomics. In Acta Crystallogr., pp. 239-249.

Debreczeni, J.E., Bunkoczi, G., Girmann, B., and Sheldrick, G.M. 2003a. In-house phase determination of the lima bean trypsin inhibitor: a low-resolution sulfur-SAD case. Acta Crystallogr. D Biol. Crystallogr. 59: 393-395.

Debreczeni, J.E., Bunkoczi, G., Ma, Q., Blaser, H., and Sheldrick, G.M. 2003b. In-house measurement of the sulfur anomalous signal and its use for phasing. Acta Crystallogr. D Biol. Crystallogr. 59: 688-696.

Doublie, S. 1997. Preparation of selenomethionyl proteins for phase determinations. In Methods Enzymol., pp. 523-530.

Emsley, P., and Cowtan, K. 2004. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60: 2126-2132.

Evans, P.R. 2001. Rotations and rotation matrices. In Acta Crystallogr., pp. 1355-1359.

Ferre-D'Amare, A.R., and Burley, S.K. 1997. Dynamic light scattering in evaluating crystallizability of macromolecules. In Methods Enzymol., pp. 157-166.

Garman, E., and Murray, J.W. 2003. Heavy-atom derivatization. In Acta Crystallogr., pp. 1903-1913.

Gonzalez, A. 2003. Optimizing data collection for structure determination. In Acta Crystallogr., pp. 1935-1942.

Grosse-Kunstleve, R.W., and Adams, P.D. 2001. Patterson correlation methods: a review of molecular replacement with CNS. In Acta Crystallogr., pp. 1390-1396.

Hendrickson, W.A. 1991. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. In Science, pp. 51-58.

Hendrickson, W.A., and Ogata, C.M. 1997. Phase determination from multiwavelength anomalous diffraction measurements. In Methods Enzymol., pp. 494-523.

Holden, H.M., and Rayment, I. 1991. Trimethyllead acetate: a first-choice heavy atom derivative for protein crystallography. In Arch. Biochem. Biophys., pp. 187-194.

Ke, H. 1997. Overview of isomorphous replacement phasing. In Methods Enzymol., pp. 448-461.

Kleywegt, G.J., and Brünger, A.T. 1996. Checking your imagination: applications of the free R value. In Structure, pp. 897-904.

Kleywegt, G.J., and Jones, T.A. 1997. Model building and refinement practice. In Methods Enzymol., pp. 208-230.

Lattman, E.E. 1996. Why are protein crystallographic R-values so high? In Proteins, pp. i-ii.

Luecke, H., Richter, H.T., and Lanyi, J.K. 1998. Proton transfer pathways in bacteriorhodopsin at 2.3 angstrom resolution. In Science, pp. 1934-1937.

Lusty, C.J. 1999. A gentle vapor-diffusion technique for cross-linking of protein crystals for cryocrystallography. In J. Appl. Cryst., pp. 106-112.

Luzzati, P.V. 1952. Traitement statistique des erreurs dans la determination des structures cristallines. In Acta Crystallogr., pp. 802-810.

McPherson, A. 1990. Current approaches to macromolecular crystallization. In Eur. J. Biochem., pp. 1-23.

Navaza, J. 2001. Implementation of molecular replacement in AMoRe. In Acta Crystallogr., pp. 1367-1372.

Parsons, S. 2003. Introduction to twinning. In Acta Crystallogr., pp. 1995-2003.

Rayment, I. 2002. Small-scale batch crystallization of proteins revisited: an underutilized way to grow large protein crystals. In Structure, pp. 147-151.

Read, R.J. 1986. Improved fourier coefficents for maps using phases from partial structures with errors. In Acta Crystallogr., pp. 140-149.

Redinbo, M.R., and Yeates, T.O. 1993. Structure determination of platocyanin from a specimen with a hemihedral twinning fraction of one-half. In Acta Crystallogr., pp. 375-380.

Rees, D.C. 1980. The influence of twinning by merohedry on intensity statistics. In Acta Crystallogr., pp. 578-581.

Rees, D.C. 1982. A general theory of X-ray intensity statistics for twins by merohedry. In Acta Crystallogr., pp. 201-207.

Rodgers, D.W. 1994. Cryocrystallography. In Structure, pp. 1135-1140.

Rodgers, D.W. 1997. Practical cryocrystallography. In Methods Enzymol., pp. 183-203.

Rould, M.A. 1997. Screening for heavy-atom derivatives and obtaining accurate isomorphous differences. In Methods Enzymol., pp. 461-472.

Schuermann, J.P., and Tanner, J.J. 2003. MRSAD: using anomalous dispersion from S atoms collected at Cu Kalpha wavelength in molecular-replacement structure determination. In Acta Crystallogr., pp. 1731-1736.

Stout, G.H., and Jensen, L.H. 1989. X-ray structure determination : a practical guide, 2nd ed. Wiley, New York, pp. xv, 453.

Stura, E.A., and Wilson, I.A. 1990. Analytical and production seeding techniques. In Methods: Companion Methods Enzymol., pp. 12-24.

Sun, P.D., Radaev, S., and Kattah, M. 2002. Generating isomorphous heavy-atom derivatives by a quick-soak method. Part I: test cases. In Acta Crystallogr., pp. 1092-1098.

Taylor, G. 2003. The phase problem. In Acta Crystallogr., pp. 1881-1890.

Tinoco, I.J., Sauer, K., Wang, J.C., and Puglisi, J.D. 2002. Physical chemistry : principles and applications in biological sciences, 4th ed. Prentice Hall, Upper Saddle River, N.J., pp. xix, 740.

Vitkup, D., Ringe, D., Karplus, M., and Petsko, G.A. 2002. Why protein R-factors are so large: a self-consistent analysis. In Proteins, pp. 345-354.

Weber, P.C. 1997. Overview of protein crystallization methods. In Methods Enzymol., pp. 13-22.

Yang, C., and Pflugrath, J.W. 2001. Applications of anomalous scattering from S atoms for improved phasing of protein diffraction data collected at Cu Kalpha wavelength. In Acta Crystallogr., pp. 1480-1490.

Yeates, T.O., and Fam, B.C. 1999. Protein crystals and their evil twins. In Structure Fold. Des., pp. R25-29.

Zulauf, M., and D'Arcy, A. 1992. Light scattering of proteins as a criterion for crystallization. In J. Cryst. Growth, pp. 102-106.