Skip to main content
SpringerLink
Log in

Acknowledging Errors: Advanced Molecular Replacement with Phaser

  • Protocol
  • First Online:
Protein Crystallography

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1607))

Abstract

Molecular replacement is a method for solving the crystallographic phase problem using an atomic model for the target structure. State-of-the-art methods have moved the field significantly from when it was first envisaged as a method for solving cases of high homology and completeness between a model and target structure. Improvements brought about by application of maximum likelihood statistics mean that various errors in the model and pathologies in the data can be accounted for, so that cases hitherto thought to be intractable are standardly solvable. As a result, molecular replacement phasing now accounts for the lion’s share of structures deposited in the Protein Data Bank. However, there will always be cases at the fringes of solvability. I discuss here the approaches that will help tackle challenging molecular replacement cases.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 279.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Tollin P (1969) Determination of the orientation and position of the myoglobin molecule in the crystal of seal myoglobin. J Mol Biol 45:481–490

    Article  CAS  PubMed  Google Scholar 

  2. Ward KB, Wishner BC, Lattman EE et al (1975) Structure of deoxyhemoglobin a crystals grown from polyethylene glycol solutions. J Mol Biol 98:161–177

    Article  CAS  PubMed  Google Scholar 

  3. Schmid MF, Herriott JR, Lattman EE (1974) The structure of bovine carboxypeptidase B: results at 5.5 Ångström resolution. J Mol Biol 84:97–101

    Article  CAS  PubMed  Google Scholar 

  4. Rossmann MG, Blow DM (1962) The detection of sub-units within the crystallographic asymmetric unit. Acta Crystallogr 15:24–31

    Article  CAS  Google Scholar 

  5. McCoy AJ (2007) Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr D Biol Crystallogr 63:32–41

    Article  CAS  PubMed  Google Scholar 

  6. Rupp B (2009) Biomolecular crystallography: principles, practice and applications to structural biology. Garland Science, New York

    Google Scholar 

  7. Brunger AT (1992) X-PLOR: version 3.1 a system for X-ray crystallography and NMR. Yale University Press, New Haven, CT

    Google Scholar 

  8. Brünger AT, Adams PD, Clore GM et al (1998) Crystallography & NMR System: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905–921

    Article  PubMed  Google Scholar 

  9. Navaza J (2001) Implementation of molecular replacement in AMoRe. Acta Crystallogr D Biol Crystallogr 57:1367–1372

    Article  CAS  PubMed  Google Scholar 

  10. Vagin A, Teplyakov A (2010) Molecular replacement with MOLREP. Acta Crystallogr D Biol Crystallogr 66:22–25

    Article  CAS  PubMed  Google Scholar 

  11. Kissinger CR, Gehlhaar DK, Fogel DB (1999) Rapid automated molecular replacement by evolutionary search. Acta Crystallogr D Biol Crystallogr 55:484–491

    Article  CAS  PubMed  Google Scholar 

  12. Glykos NM, Kokkinidis M (2001) Multidimensional molecular replacement. Acta Crystallogr D Biol Crystallogr 57:1462–1473

    Article  CAS  PubMed  Google Scholar 

  13. Jamrog DC, Zhang Y, Phillips GN (2003) SOMoRe: a multi-dimensional search and optimization approach to molecular replacement. Acta Crystallogr D Biol Crystallogr 59:304–314

    Article  PubMed  CAS  Google Scholar 

  14. Jogl G, Tao X, Xu Y, Tong L (2001) COMO: a program for combined molecular replacement. Acta Crystallogr D Biol Crystallogr 57:1127–1134

    Article  CAS  PubMed  Google Scholar 

  15. McCoy AJ, Grosse-Kunstleve RW, Adams PD et al (2007) Phaser crystallographic software. J Appl Cryst 40:658–674

    Article  CAS  Google Scholar 

  16. Toth EA (2007) Molecular replacement. Methods Mol Biol 364:121–148

    CAS  PubMed  Google Scholar 

  17. Berman H, Henrick K, Nakamura H (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10:980

    Article  CAS  PubMed  Google Scholar 

  18. Scapin G (2013) Molecular replacement then and now. Acta Crystallogr D Biol Crystallogr 69:2266–2275

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Marcia M, Humphris-Narayanan E, Keating KS et al (2013) Solving nucleic acid structures by molecular replacement: examples from group II intron studies. Acta Crystallogr D Biol Crystallogr 69:2174–2185

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Read RJ, McCoy AJ (2016) A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error. Acta Crystallogr D Biol Crystallogr 72:375–387

    Article  CAS  Google Scholar 

  21. Read RJ (2001) Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr D Biol Crystallogr 57:1373–1382

    Article  CAS  PubMed  Google Scholar 

  22. French S, Wilson K (1978) On the treatment of negative intensity observations. Acta Crystallogr A 34:517–525

    Article  Google Scholar 

  23. Winn MD, Ballard CC, Cowtan KD et al (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67:235–242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Adams PD, Afonine PV, Bunkóczi G et al (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66:213–221

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Potterton E, Briggs P, Turkenburg M, Dodson E (2003) A graphical user interface to the CCP 4 program suite. Acta Crystallogr D Biol Crystallogr 59:1131–1137

    Article  PubMed  Google Scholar 

  26. Echols N, Grosse-Kunstleve RW, Afonine PV et al (2012) Graphical tools for macromolecular crystallography in PHENIX. J Appl Cryst 45:581–586

    Article  CAS  Google Scholar 

  27. Keegan RM, Winn MD (2008) MrBUMP: an automated pipeline for molecular replacement. Acta Crystallogr D Biol Crystallogr 64:119–124

    Article  CAS  PubMed  Google Scholar 

  28. Bunkóczi G, Echols N, McCoy AJ et al (2013) Phaser.MRage: Automated molecular replacement. Acta Crystallogr D Biol Crystallogr 69:2276–2286

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. Stokes-Rees I, Sliz P (2010) Protein structure determination by exhaustive search of Protein Data Bank derived databases. Proc Natl Acad Sci U S A 107:21476–21481

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Strong M, Sawaya MR, Wang S et al (2006) Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 103:8060–8065

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Rodríguez DD, Grosse C, Himmel S et al (2009) Crystallographic ab initio protein structure solution below atomic resolution. Nat Methods 6:651–653

    Article  PubMed  CAS  Google Scholar 

  32. Bibby J, Keegan RM, Mayans O et al (2012) AMPLE: A cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed ab initio models. Acta Crystallogr D Biol Crystallogr 68:1622–1631

    Article  CAS  PubMed  Google Scholar 

  33. Wilson AJC (1942) Determination of absolute from relative X-ray intensity data. Nature 150:152

    Article  Google Scholar 

  34. McCoy AJ, Oeffner RD, Wrobel AG, Ojala JRM, Tryggvason K, Lohkamp B, Read RJ (2017) Ab initio solution of macromolecular crystal structures without direct methods. Proc Natl Acad Sci U S A 114:3637–3641

    Google Scholar 

  35. McCoy AJ, Read RJ, BunkĂłczi G et al Phaserwiki. http://www.phaser.cimr.cam.ac.uk

  36. Evans P, McCoy A (2008) An introduction to molecular replacement. Acta Crystallogr D Biol Crystallogr 64:1–10

    Article  CAS  PubMed  Google Scholar 

  37. Ten Eyck LF (1973) Crystallographic fast Fourier transforms. Acta Crystallogr A 29:183–191

    Article  Google Scholar 

  38. Storoni LC, McCoy AJ, Read RJ (2004) Likelihood-enhanced fast rotation functions. Acta Crystallogr D Biol Crystallogr 60:432–438

    Article  PubMed  CAS  Google Scholar 

  39. McCoy AJ, Grosse-Kunstleve RW, Storoni LC et al (2005) Likelihood-enhanced fast translation functions. Acta Crystallogr D Biol Crystallogr 61:458–464

    Article  PubMed  CAS  Google Scholar 

  40. Oeffner RD, Bunkóczi G, McCoy AJ et al (2013) Improved estimates of coordinate error for molecular replacement. Acta Crystallogr D Biol Crystallogr 69:2209–2215

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Long F, Vagin AA, Young P et al (2008) BALBES: a molecular-replacement pipeline. Acta Crystallogr D Biol Crystallogr 64:125–132

    Article  CAS  PubMed  Google Scholar 

  42. Rosetta Commons. https://www.rosettacommons.org/about/pubs

  43. DiMaio F, Echols N, Headd JJ et al (2013) Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nat Methods 10:1102–1104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Pedersen BP, Gourdon P, Liu X et al (2016) Initiating heavy-atom-based phasing by multi-dimensional molecular replacement. Acta Crystallogr D Biol Crystallogr 72:440–445

    Article  CAS  Google Scholar 

  45. Urzhumtseva L, Urzhumtsev A (2002) COMPANG: automated comparison of orientations. J Appl Cryst 35:644–647

    Article  CAS  Google Scholar 

  46. Buehler A, Urzhumtseva L, Lunin VY et al (2009) Cluster analysis for phasing with molecular replacement: a feasibility study. Acta Crystallogr D Biol Crystallogr 65:644–650

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Millán C, Sammito M, Garcia-Ferrer I, Goulas T, Sheldrick GM, Usón I (2015) Combining phase information in reciprocal space for molecular replacement with partial models. Acta Crystallogr D 71:1931–1945

    Google Scholar 

  48. Phillips DC, Rogers D, Wilson AJC (1950) Reliability index for centrosymmetric and non-centrosymmetric structures. Acta Crystallogr 3:398–399

    Article  Google Scholar 

  49. Navaza J (1994) AMoRe : an automated package for molecular replacement. Acta Crystallogr A 50:157–163

    Google Scholar 

  50. Fujinaga M, Read RJ (1987) Experiences with a new translation-function program. J Appl Cryst 20:517–521

    Article  Google Scholar 

  51. Delarue M (2007) Molecular replacement techniques for high-throughput structure determination. In: Sanderson MR, Skelly JV (eds) Macromolecular crystallography: conventional and high-throughput methods. Oxford University Press, Oxford

    Google Scholar 

  52. Abergel C (2013) Molecular replacement: tricks and treats. Acta Crystallogr D Biol Crystallogr 69:2167–2173

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Turkenburg JP, Dodson EJ (1996) Modern developments in molecular replacement. Curr Opin Struct Biol 6:604–610

    Article  CAS  PubMed  Google Scholar 

  54. Dodson E (2008) The befores and afters of molecular replacement. Acta Crystallogr D Biol Crystallogr 64:17–24

    Article  CAS  PubMed  Google Scholar 

  55. Schwarzenbacher R, Godzik A, Grzechnik SK et al (2004) The importance of alignment accuracy for molecular replacement. Acta Crystallogr D Biol Crystallogr 60:1229–1236

    Article  PubMed  CAS  Google Scholar 

  56. Qian B, Raman S, Das R et al (2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450:259–264

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Bahar I, Atilgan AR, Erman B (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 2:173–181

    Article  CAS  PubMed  Google Scholar 

  58. Haliloglu T, Bahar I (1999) Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data. Proteins 37:654–667

    Article  CAS  PubMed  Google Scholar 

  59. Tirion M (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 77:1905–1908

    Article  CAS  PubMed  Google Scholar 

  60. Tama F, Sanejouand YH (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng 14:1–6

    Article  CAS  PubMed  Google Scholar 

  61. Krebs WG, Alexandrov V, Wilson CA et al (2002) Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins 48:682–695

    Article  CAS  PubMed  Google Scholar 

  62. Suhre K, Sanejouand YH (2004) On the potential of normal-mode analysis for solving difficult molecular-replacement problems. Acta Crystallogr D Biol Crystallogr 60:796–799

    Article  PubMed  CAS  Google Scholar 

  63. Blaszczyk J, Li Y, Yan H et al (2001) Crystal structure of unligated guanylate kinase from yeast reveals GMP-induced conformational changes. J Mol Biol 307:247–257

    Article  CAS  PubMed  Google Scholar 

  64. SBGrid Science Portal. https://portal.sbgrid.org/d/apps/wsmr/docs

  65. Zhou A, Carrell RW, Murphy MP et al (2010) A redox switch in angiotensinogen modulates angiotensin release. Nature 468:108–111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Tronrud DE (1997) TNT refinement package. Methods Enzymol 277:306–319

    Article  CAS  PubMed  Google Scholar 

  67. Fokine A, Capitani G, Grütter MG et al (2003) Bulk-solvent correction for fast translation search in molecular replacement: service programs for AMoRe and CNS. J Appl Cryst 36:352–355

    Article  CAS  Google Scholar 

  68. Jackson RN, McCoy AJ, Terwilliger TC et al (2015) X-ray structure determination using low-resolution electron microscopy maps for molecular replacement. Nat Protoc 10:1275–1284

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Stein N (2008) CHAINSAW : a program for mutating pdb files used as templates in molecular replacement. J Appl Cryst 41:641–643

    Google Scholar 

  70. Bunkóczi G, Read RJ (2011) Improvement of molecular-replacement models with Sculptor. Acta Crystallogr D Biol Crystallogr 67:303–312

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  71. Wriggers W, Schulten K (1997) Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins 29:1–14

    Article  CAS  PubMed  Google Scholar 

  72. Hayward S, Berendsen HJ (1998) Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins 30:144–154

    Article  CAS  PubMed  Google Scholar 

  73. Schneider TR (2000) Objective comparison of protein structures: error-scaled difference distance matrices. Acta Crystallogr D Biol Crystallogr 56:714–721

    Article  CAS  PubMed  Google Scholar 

  74. McCoy AJ, Nicholls RA, Schneider TR (2013) SCEDS: protein fragments for molecular replacement in Phaser. Acta Crystallogr D Biol Crystallogr 69:2216–2225

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Wodak SJ, Janin J (1980) Analytical approximation to the accessible surface area of proteins. Proc Natl Acad Sci U S A 77:1736–1740

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Painter J, Merritt EA (2006) Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr D Biol Crystallogr 62:439–450

    Article  PubMed  CAS  Google Scholar 

  77. Hinsen K (1998) Analysis of domain motions by approximate normal mode calculations. Proteins 33:417–429

    Article  CAS  PubMed  Google Scholar 

  78. Thomas JMH, Keegan RM, Bibby J et al (2015) Routine phasing of coiled-coil protein crystal structures with AMPLE. IUCr J 2:198–206

    Article  CAS  Google Scholar 

  79. Sammito M, Millán C, Rodríguez DD et al (2013) Exploiting tertiary structure through local folds for crystallographic phasing. Nat Methods 10:1099–1101

    Article  CAS  PubMed  Google Scholar 

  80. Sammito M, Meindl K, de Ilarduya IM et al (2014) Structure solution with ARCIMBOLDO using fragments derived from distant homology models. FEBS J 281:4029–4045

    Article  CAS  PubMed  Google Scholar 

  81. Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5:823–826

    CAS  PubMed  PubMed Central  Google Scholar 

  82. Bunkóczi G, Wallner B, Read RJ (2015) Local error estimates dramatically improve the utility of homology models for solving crystal structures by molecular replacement. Structure 23:397–406

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  83. Brünger AT (1993) Structure determination of antibodies and antibody-antigen complexes by molecular replacement. Immunomethods 3:180–190

    Article  Google Scholar 

  84. Stanfield RL, Zemla A, Wilson IA et al (2006) Antibody elbow angles are influenced by their light chain class. J Mol Biol 357:1566–1574

    Article  CAS  PubMed  Google Scholar 

  85. Almagro JC, Beavers MP, Hernandez-Guzman F et al (2011) Antibody modeling assessment. Proteins 79:3050–3066

    Article  CAS  PubMed  Google Scholar 

  86. Griffin L, Lawson A (2011) Antibody fragments as tools in crystallography. Clin Exp Immunol 165:285–291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Tollin P, Rossmann MG (1966) A description of various rotation function programs. Acta Crystallogr 21:872–876

    Article  CAS  PubMed  Google Scholar 

  88. Jeffery P Molecular replacement guide. http://xray0.princeton.edu/~phil/Facility/Guides/MolecularReplacement.html

  89. Ling H, Boodhoo A, Hazes B et al (1998) Structure of the shiga-like toxin I B-pentamer complexed with an analogue of its receptor Gb3. Biochemistry 37:1777–1788

    Article  CAS  PubMed  Google Scholar 

  90. Karplus PA, Diederichs K (2012) Linking crystallographic model and data quality. Science 336:1030–1033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Matthews BW (1968) Solvent content of protein crystals. J Mol Biol 33:491–497

    Article  CAS  PubMed  Google Scholar 

  92. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Weichenberger CX, Rupp B (2014) Ten years of probabilistic estimates of biocrystal solvent content: new insights via nonparametric kernel density estimate. Acta Crystallogr D Biol Crystallogr 70:1579–1588

    Article  CAS  PubMed  Google Scholar 

  94. Sawaya MR (2007) Characterizing a crystal from an initial native dataset. Methods Mol Biol 364:95–120

    CAS  PubMed  Google Scholar 

  95. Read RJ, Adams PD, McCoy AJ (2013) Intensity statistics in the presence of translational noncrystallographic symmetry. Acta Crystallogr D Biol Crystallogr 69:176–183

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Kleywegt GJ, Read RJ (1997) Not your average density. Structure 5:1557–1569

    Article  CAS  PubMed  Google Scholar 

  97. Lebedev AA, Vagin AA, Murshudov GN (2006) Intensity statistics in twinned crystals with examples from the PDB. Acta Crystallogr D Biol Crystallogr 62:83–95

    Article  PubMed  CAS  Google Scholar 

  98. Yeates TO, Fam BC (1999) Protein crystals and their evil twins. Structure 7:R25–R29

    Article  CAS  PubMed  Google Scholar 

  99. Sliwiak J, Jaskolski M, Dauter Z et al (2014) Likelihood-based molecular-replacement solution for a highly pathological crystal with tetartohedral twinning and sevenfold translational noncrystallographic symmetry. Acta Crystallogr D Biol Crystallogr 70:471–480

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Evans P (2006) Scaling and assessment of data quality. Acta Crystallogr D Biol Crystallogr 62:72–82

    Article  PubMed  CAS  Google Scholar 

  101. Zwart PH, Grosse-Kunstleve RW, Adams PD (2005) Xtriage and Fest: automatic assessment of X-ray data and substructure structure factor estimation. CCP4 Newsl 43:27–35

    Google Scholar 

  102. Lebedev AA, Isupov MN (2014) Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the program Zanuda. Acta Crystallogr D Biol Crystallogr 70:2430–2443

    Article  CAS  PubMed  Google Scholar 

  103. Herbst-Irmer R, Sheldrick GM (1998) Refinement of twinned structures with SHELXL97. Acta Crystallogr B 54:443–449

    Article  Google Scholar 

  104. Dauter Z (2003) Twinned crystals and anomalous phasing. Acta Crystallogr D Biol Crystallogr 59:2004–2016

    Article  PubMed  Google Scholar 

  105. Harada Y, Lifchitz A, Berthou J et al (1981) A translation function combining packing and diffraction information: an application to lysozyme (high-temperature form). Acta Crystallogr A 37:398–406

    Article  Google Scholar 

  106. Vagin A, Teplyakov A (1997) MOLREP : an automated program for molecular replacement. J Appl Cryst 30:1022–1025

    Google Scholar 

  107. Navaza J, Vernoslova E (1995) On the fast translation functions for molecular replacement. Acta Crystallogr A 51:445–449

    Article  Google Scholar 

  108. Wang BC (1985) Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol 115:90–112

    Article  CAS  PubMed  Google Scholar 

  109. Bai X, McMullan G, Scheres SH (2014) How cryo-EM is revolutionizing structural biology. Trends Biochem Sci 40:49–57

    Article  PubMed  CAS  Google Scholar 

  110. Rossmann MG (1972) The molecular replacement method. Gordon & Breach, New York, NY

    Google Scholar 

  111. Rossmann MG (2001) Molecular replacement – historical background. Acta Crystallogr D Biol Crystallogr 57:1360–1366

    Google Scholar 

  112. Vagin AA, Isupov MN (2001) Spherically averaged phased translation function and its application to the search for molecules and fragments in electron-density maps. Acta Crystallogr D Biol Crystallogr 57:1451–1456

    Article  CAS  PubMed  Google Scholar 

  113. Colman PM, Fehlhammer H (1976) The use of rotation and translation functions in the interpretation of low resolution electron density maps. J Mol Biol 100:278–282

    Article  CAS  PubMed  Google Scholar 

  114. Schuermann JP, Tanner JJ (2003) MRSAD: using anomalous dispersion from S atoms collected at Cu Kα wavelength in molecular-replacement structure determination. Acta Crystallogr D Biol Crystallogr 59:1731–1736

    Article  PubMed  Google Scholar 

  115. Niedzialkowska E, Gasiorowska O, Handing KB et al (2016) Protein purification and crystallization artifacts: The tale usually not told. Protein Sci 25:720–733

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Hungler A, Momin A, Diederichs K, Arold ST (2016) ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants. J Appl Cryst 46:2252–2258

    Google Scholar 

  117. Rice SO (1945) Mathematical analysis of random noise. Bell Syst Tech J 24:46–156

    Article  Google Scholar 

Download references

Acknowledgments

I thank Isabel Usón for content suggestions and for proposing the title, and Randy Read for critical reading of the manuscript, discussions, and for the concept for Fig. 1. This work was supported by grant BB/L006014/1 from the BBSRC, UK.

Author information

Authors and Affiliations

  1. Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK

    Airlie J. McCoy

Authors
  1. Airlie J. McCoy
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Airlie J. McCoy .

Editor information

Editors and Affiliations

  1. Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland, USA

    Alexander Wlodawer

  2. Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, Illinois, USA

    Zbigniew Dauter

  3. Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland

    Mariusz Jaskolski

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

McCoy, A.J. (2017). Acknowledging Errors: Advanced Molecular Replacement with Phaser. In: Wlodawer, A., Dauter, Z., Jaskolski, M. (eds) Protein Crystallography. Methods in Molecular Biology, vol 1607. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7000-1_18

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7000-1_18

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6998-2

  • Online ISBN: 978-1-4939-7000-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation