Airlie J. McCoy

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Protein Crystallography with Coffee

Notes for protein crystallography students, written for the MRC-LMB Crystallography Course 2009

• Protein Crystallography with Coffee (Low Resolution Graphics 2.7MB)
• Protein Crystallography with Coffee (High Resolution Graphics 8.1MB)

These notes give an introduction to protein crystallography. The title "Protein Crystallography with Coffee" comes about because each section is designed to be read while drinking a cup of coffee (or tea!). At about 6000 words, it should take the average scientific reader 20 minutes to finish "sipping" a section. With five sections, it should only take a week of coffee breaks to finish reading.

This could be considered a postmodern approach to crystallography. It mixes the science with history and anecdotes to describe not only the "what and why" but also the "who and when".

Enjoy!

Publications

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard

Terwilliger TC, Adams PD, Read RJ, McCoy AJ , Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW.

Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):582-601

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A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex

Kelly BT, McCoy AJ, Späte K, Miller SE, Evans PR, Höning S, Owen DJ.

Nature. 2008 Dec 18;456(7224):976-79

Nature (subscription required)

An introduction to molecular replacement

Evans P, McCoy A.

Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):1-10. Epub 2007 Dec 5.

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Automated structure solution with the PHENIX suite

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.

Methods Mol Biol. 2008;426:419-35.

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A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles

Miller SE, Collins BM, McCoy AJ, Robinson MS, Owen DJ.

Nature. 2007 Nov 22;450(7169):570-4

Nature (subscription required)

High-resolution structure prediction and the crystallographic phase problem

Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D.

Nature. 2007 Nov 8;450(7167):259-64. Epub 2007 Oct 14.

Nature (subscription required)

β-Edge interactions in a pentadecameric human antibody Vκ domain.

James LC, Jones PC, McCoy A, Tennent GA, Pepys MB, Famm K, Winter G.

J Mol Biol. 2007 Mar 30;367(3):603-8. Epub 2006 Nov 3.

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Phaser crystallographic software

McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC and Read RJ.

J. Appl. Cryst. (2007). 40, 658-674.

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Solving structures of protein complexes by molecular replacement with Phaser

McCoy AJ

Acta Crystallogr D Biol Crystallogr. 2007 Jan;63(Pt 1):32-41. Epub 2006 Dec 13.

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Crystal structure of rab11 in complex with rab11 family interacting protein 2

Jagoe WN, Lindsay AJ, Read RJ, McCoy AJ, McCaffrey MW, Khan AR.

Structure. 2006 Aug;14(8):1273-83.

Structure (subscription required)

Likelihood-enhanced fast translation functions

McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ.

Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):458-64. Epub 2005 Mar 24.

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Liking Likelihood

McCoy AJ

Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2169-83. Epub 2004 Nov 26.

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Simple algorithm for a maximum-likelihood SAD function

McCoy AJ, Storoni LC, Read RJ.

Acta Crystallogr D Biol Crystallogr. 2004 Jul;60(Pt 7):1220-8. Epub 2004 Jun 22.

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Likelihood-enhanced fast rotation functions

Storoni LC, McCoy AJ, Read RJ.

Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8. Epub 2004 Feb 25.

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Recent developments in the PHENIX software for automated crystallographic structure determination

Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC.

J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):53-5. Epub 2003 Nov 28.

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Application of the complex multivariate normal distribution to crystallographic methods with insights into multiple isomorphous replacement phasing

Pannu NS, McCoy AJ, Read RJ.

Acta Crystallogr D Biol Crystallogr. 2003 Oct;59(Pt 10):1801-8. Epub 2003 Sep 19.

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Structure of β-antithrombin and the effect of glycosylation on antithrombin's heparin affinity and activity

McCoy AJ, Pei XY, Skinner R, Abrahams JP, Carrell RW.

J Mol Biol. 2003 Feb 21;326(3):823-33.

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New applications of maximum likelihood and Bayesian statistics in macromolecular crystallography

McCoy AJ

Curr Opin Struct Biol. 2002 Oct;12(5):670-3. Review.

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PHENIX: building new software for automated crystallographic structure determination

Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC.

Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54. Epub 2002 Oct 21.

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Molecular architecture and functional model of the endocytic AP2 complex

Collins BM, McCoy AJ, Kent HM, Evans PR, Owen DJ.

Cell. 2002 May 17;109(4):523-35.

Cell (subscription required)

ScFv multimers of the anti-neuraminidase antibody NC10: shortening of the linker in single-chain Fv fragment assembled in V(L) to V(H) orientation drives the formation of dimers, trimers, tetramers and higher molecular mass multimers

Dolezal O, Pearce LA, Lawrence LJ, McCoy AJ, Hudson PJ, Kortt AA.

Protein Eng. 2000 Aug;13(8):565-74.

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The conformational activation of antithrombin. A 2.85-A structure of a fluorescein derivative reveals an electrostatic link between the hinge and heparin binding regions.

Huntington JA*, McCoy A*, Belzar KJ, Pei XY, Gettins PG, Carrell RW.

*authors contributed equally

J Biol Chem. 2000 May 19;275(20):15377-83

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Structural basis for dimerization of the Dictyostelium gelation factor (ABP120) rod

McCoy AJ, Fucini P, Noegel AA, Stewart M.

Nat Struct Biol. 1999 Sep;6(9):836-41.

Nature Structural Biology (subscription required)

scFv multimers of the anti-neuraminidase antibody NC10: length of the linker between VH and VL domains dictates precisely the transition between diabodies and triabodies

Atwell JL, Breheney KA, Lawrence LJ, McCoy AJ, Kortt AA, Hudson PJ.

Protein Eng. 1999 Jul;12(7):597-604.

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Engineered mutants in the switch II loop of Ran define the contribution made by key residues to the interaction with nuclear transport factor 2 (NTF2) and the role of this interaction in nuclear protein import

Kent HM, Moore MS, Quimby BB, Baker AM, McCoy AJ, Murphy GA, Corbett AH, Stewart M.

J Mol Biol. 1999 Jun 11;289(3):565-77.

doi Digital Object Identifier

The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2)

Stewart M, Kent HM, McCoy AJ.

J Mol Biol. 1998 Dec 18;284(5):1517-27.

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Three-dimensional structures of single-chain Fv-neuraminidase complexes

Malby RL*, McCoy AJ*, Kortt AA, Hudson PJ, Colman PM.

*authors contributed equally

J Mol Biol. 1998 Jun 19;279(4):901-10.

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Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran

Stewart M, Kent HM, McCoy AJ.

J Mol Biol. 1998 Apr 3;277(3):635-46.

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Structural basis for amoeboid motility in nematode sperm

Bullock TL, McCoy AJ, Kent HM, Roberts TM, Stewart M.

Nat Struct Biol. 1998 Mar;5(3):184-9.

Nature Structural Biology (subscription required)

Crystallization and preliminary X-Ray diffraction characterization of a dimerizing fragment of the rod domain of the Dictyostelium gelation factor (ABP-120)

Fucini P, McCoy AJ, Gomez-Ortiz M, Schleicher M, Noegel AA, Stewart M.

J Struct Biol. 1997 Nov;120(2):192-5

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Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran

Clarkson WD, Corbett AH, Paschal BM, Kent HM, McCoy AJ, Gerace L, Silver PA, Stewart M.

J Mol Biol. 1997 Oct 10;272(5):716-30.

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The 1.8 Å crystal structure of winged bean albumin 1, the major albumin from Psophocarpus tetragonolobus (L.) DC

McCoy AJ, Kortt AA.

J Mol Biol. 1997 Jun 27;269(5):881-91.

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Electrostatic complementarity at protein/protein interfaces

McCoy AJ, Chandana Epa V, Colman PM.

J Mol Biol. 1997 May 2;268(2):570-84.

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Single-chain Fv fragments of anti-neuraminidase antibody NC10 containing five- and ten-residue linkers form dimers and with zero-residue linker a trimer

Kortt AA, Lah M, Oddie GW, Gruen CL, Burns JE, Pearce LA, Atwell JL, McCoy AJ, Howlett GJ, Metzger DW, Webster RG, Hudson PJ.

Protein Eng. 1997 Apr;10(4):423-33.

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Not the Real McCoys There are four other AJ McCoys publishing in biomedical science and cited in PubMed Andrea J. McCoy − University of Texas, TX USA and F Edward Hébert School of Medicine, Bethesda, MD USA Almedia J. McCoy − East Carolina University, Greenville, NC USA Austin J. McCoy − Vanderbilt University, Nashville, TN USA A. Jeanene McCoy − Disney's Animal Programs, Walt Disney World Resort, FL USA Thus an author search for McCoy AJ in PubMed will lead to a combined publication list for all five of us.