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