Phasing electron diffraction data by molecular replacement: Strategy for structure determination and refinement

Methods in Molecular Biology

Volumn 955, Issue , 2013, Pages 243-272

  Wisedchaisri, Goragot ^a   Gonen, Tamir ^a  

^a NONE

Author keywords

Electron cryomicroscopy (Cryo EM); Electron crystallography; Electron diffraction; Molecular replacement; Structure refinement

Indexed keywords

CRYOELECTRON MICROSCOPY; CRYSTALLOGRAPHY; ELECTRON DIFFRACTION; HUMAN TISSUE; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; INSTRUMENTATION; METHODOLOGY; PROTEIN DATABASE;

MEMBRANE PROTEIN;

COMPUTATIONAL BIOLOGY; CRYOELECTRON MICROSCOPY; CRYSTALLOGRAPHY; DATABASES, PROTEIN; MEMBRANE PROTEINS; MODELS, MOLECULAR; SOFTWARE;

EID: 84876030085     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-176-9_14     Document Type: Chapter

References (43)

1. Henderson R, Unwin PN (1975) Three- dimensional model of purple membrane obtained by electron microscopy. Nature 257:28–32
2. Fujiyoshi Y (1998) The structural study of membrane proteins by electron crystallography. Adv Biophys 35:25–80
3. Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, Harrison SC, Walz T (2005) Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature 438:633–638
4. Hite RK, Li Z, Walz T (2010) Principles of membrane protein interactions with annular lipids deduced from aquaporin-0 2D crystals. EMBO J 29:1652–1658
5. Mitsuoka K, Hirai T, Murata K, Miyazawa A, Kidera A, Kimura Y, Fujiyoshi Y (1999) The structure of bacteriorhodopsin at 3.0 A resolution based on electron crystallography: implication of the charge distribution. J Mol Biol 286:861–882
6. Tani K, Mitsuma T, Hiroaki Y, Kamegawa A, Nishikawa K, Tanimura Y, Fujiyoshi Y (2009) Mechanism of aquaporin-4’s fast and highly selective water conduction and proton exclusion. J Mol Biol 389:694–706
7. Crowther RA, Henderson R, Smith JM (1996) MRC image processing programs. J Struct Biol 116:9–16
8. Gipson B, Zeng X, Stahlberg H (2007) 2dx_ merge: data management and merging for 2D crystal images. J Struct Biol 160:375–384
9. Philippsen A, Schenk AD, Signorell GA, Mariani V, Berneche S, Engel A (2007) Collaborative EM image processing with the IPLT image processing library and toolbox. J Struct Biol 157:28–37
10. Ceska TA, Henderson R (1990) Analysis of high-resolution electron diffraction patterns from purple membrane labelled with heavyatoms. J Mol Biol 213:539–560
11. Gonen T, Sliz P, Kistler J, Cheng Y, Walz T (2004) Aquaporin-0 membrane junctions reveal the structure of a closed water pore. Nature 429:193–197
12. Navaza J (1994) Amore—an automated package for molecular replacement. Acta Crystallogr A50:157–163
13. Trapani S, Navaza J (2008) AMoRe: classical and modern. Acta Crystallogr D64:11–16
14. Vagin A, Teplyakov A (1997) MOLREP: an automated program for molecular replacement. J Appl Crystallogr 30:1022–1025
15. Vagin A, Teplyakov A (2010) Molecular replacement with MOLREP. Acta Crystallogr D66:22–25
16. McCoy AJ (2007) Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr D63:32–41
17. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) Phaser crystallographic software. J Appl Crystallogr 40:658–674
18. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D50:760–763
19. Brunger AT (2007) Version 1.2 of the crystallography and NMR system. Nat Protoc 2:2728–2733
20. 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 (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D54:905–921
21. Potterton E, Briggs P, Turkenburg M, Dodson E (2003) A graphical user interface to the CCP4 program suite. Acta Crystallogr D59:1131–1137
22. Stein N (2008) CHAINSAW: a program for mutating pdb files used as templates in molecular replacement. J Appl Crystallogr 41:641–643
23. Vagin A, Teplyakov A (2000) An approach to multi-copy search in molecular replacement. Acta Crystallogr D56:1622–1624
24. Tong L (2001) How to take advantage of non- crystallographic symmetry in molecular replacement: ‘locked’ rotation and translation functions. Acta Crystallogr D57:1383–1389
25. Tong L, Rossmann MG (1990) The locked rotation function. Acta Crystallogr A46:783–792
26. Tong LA (1996) The locked translation function and other applications of a Patterson correlation function. Acta Crystallogr A52:476–479
27. Long F, Vagin AA, Young P, Murshudov GN (2008) BALBES: a molecular-replacement pipeline. Acta Crystallogr D64:125–132
28. Keegan RM, Winn MD (2008) MrBUMP: an automated pipeline for molecular replacement. Acta Crystallogr D64:119–124
29. Sui HX, Han BG, Lee JK, Walian P, Jap BK (2001) Structural basis of water-specific transport through the AQP1 water channel. Nature 414:872–878
30. Vaguine AA, Richelle J, Wodak SJ (1999) SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D55:191–205
31. French S, Wilson K (1978) Treatment of negative intensity observations. Acta Crystallogr A34:517–525
32. Matthews BW (1968) Solvent content of protein crystals. J Mol Biol 33:491–497
33. Kantardjieff KA, Rupp B (2003) Matthews coefficient probabilities: improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Protein Sci 12:1865–1871
34. Teneyck LF (1973) Crystallographic fast Fouriertransforms. Acta Crystallogr A29:183–191
35. Lebedev AA, Vagin AA, Murshudov GN (2008) Model preparation in MOLREP and examples of model improvement using X-ray data. Acta Crystallogr D64:33–39
36. Emsley P, Cowtan K (2004) Coot: modelbuilding tools for molecular graphics. Acta Crystallogr D60:2126–2132
37. Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D66:486–501
38. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D53:240–255
39. Cohen SX, Ben Jelloul M, Long F, Vagin A, Knipscheer P, Lebbink J, Sixma TK, Lamzin VS, Murshudov GN, Perrakis A (2008) ARP/ wARP and molecular replacement: the next generation. Acta Crystallogr D64:49–60
40. Perrakis A, Harkiolaki M, Wilson KS, Lamzin VS (2001) ARP/wARP and molecular replacement. Acta Crystallogr D57:1445–1450
41. Terwilliger TC (2003) Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement. Acta Crystallogr D59:1174–1182
42. Terwilliger TC (2003) Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr D59:38–44
43. Terwilliger TC (2003) Automated side-chain model building and sequence assignment by template matching. Acta Crystallogr D59:45–49