Abstract
Molecular replacement is already able to solve the majority of structures in the Protein Data Bank, thanks to the rapidly increasing number of template structures available and continuous improvements in the algorithms. Chances of success can be optimised by proper preparation of models, for instance by trimming poorly-conserved regions, creating an ensemble of alternative models or applying advanced homology modeling tools. The sensitivity of the molecular replacement search can be improved by using likelihood targets; these lend themselves to automation, which makes it possible to carry out extensive searches and helps to avoid user errors. The convergence radius of model completion can be extended by using methods that smoothly deform the starting model or apply advanced modeling techniques. Even more difficult structures can be solved by combining molecular replacement with other phasing methods, such as SAD phasing or multi-crystal averaging.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D 66:213–221
Brunger AT, Das D, Deacon AM, Grant J, Terwilliger TC, Read RJ, Adams PD, Levitt M, Schröder GF (2012) Application of DEN-refinement and automated model-building to a difficult case of molecular replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum. Acta Crystallogr D 68:391–403
Bunkóczi G, Read RJ (2011) Improvement of molecular replacement models with Sculptor. Acta Crystallogr D 67:303–312
DiMaio F, Terwilliger TC, Read RJ, Wlodawer A, Oberdorfer G, Wagner U, Valkov E, Alon A, Fass D, Axelrod HL, Das D, Vorobiev SM, Iwaï H, Pokkuluri PR, Baker D (2011) Improving molecular replacement by density- and energy-guided protein structure optimization. Nature 473:540–543
Glykos NM, Kokkinidis M (2001) Multidimensional molecular replacement. Acta Crystallogr D 57:1462–1473
Keegan RM, Winn MD (2008) MrBUMP: an automated pipeline for molecular replacement. Acta Crystallogr D 64:119–124
Kendrew JC, Bodo G, Dintzis HM, Parrish RG, Wyckoff H, Phillips DC (1958) A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature 181:662–666
Kissinger CR, Gehlhaar DK, Fogel DB (1999) Rapid automated molecular replacement by evolutionary search. Acta Crystallogr D 55:484–491
Lebedev AA, Vagin AA, Murshudov G (2008) Model preparation in MOLREP and examples of model improvements using X-ray data. Acta Crystallogr D 64:33–39
Long F, Vagin AA, Young P, Murshudov G (2007) BALBES: a molecular-replacement pipeline. Acta Crystallogr D 64:125–132
McCoy AJ (2004) Liking likelihood. Acta Crystallogr D 60:2169–2183
McCoy AJ, Read RJ (2010) Experimental phasing: best practice and pitfalls. Acta Crystallogr D 66:458–469
McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ (2005) Likelihood-enhanced fast translation functions. Acta Crystallogr D 61:458–464
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) Phaser crystallographic software. J Appl Crystallogr 40:658–674
Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D 67:355–367
Perutz MF, Rossmann MG, Cullis AF, Muirhead H, Will G, North AC (1960) Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-Å resolution, obtained by X-ray analysis. Nature 185:416–422
Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D (2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450:259–264
Read RJ (2001) Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr D 57:1373–1382
Read RJ, McCoy AJ (2011) Using SAD data in Phaser. Acta Crystallogr D 67:338–344
Rigden DJ, Keegan RM, Winn MD (2008) Molecular replacement using ab initio polyalanine models generated with ROSETTA. Acta Crystallogr D 64:1288–1291
Rodríguez DD, Grosse C, Himmel S, González C, de Ilarduya IM, Becker S, Sheldrick GM, Usón I (2009) Crystallographic ab initio protein structure solution below atomic resolution. Nat Methods 6:651–653
Rossmann MG (1972) The molecular replacement method. Gordon & Breach, New York
Schröder GF, Levitt M, Brunger AT (2010) Super-resolution biomolecular crystallography with low-resolution data. Nature 464:1218–1222
Schwarzenbacher R, Godzik A, Grzechnik SK, Jaroszewski L (2004) The importance of alignment accuracy for molecular replacement. Acta Crystallogr D 60:1229–1236
Storoni LC, McCoy AJ, Read RJ (2004) Likelihood-enhanced fast rotation functions. Acta Crystallogr D 60:432–438
Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Zwart PH, Hung L-W, Read RJ, Adams PD (2008) Iterative model building, structure refinement and density modification with the Phenix AutoBuild wizard. Acta Crystallogr D 64:61–69
Terwilliger TC, DiMaio F, Read RJ, Baker D, Bunkóczi G, Adams PD, Grosse-Kunstleve RW, Afonine PV, Echols N (2012) phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. J Struct Funct Genomics 13(2):81–90. doi:10.1007/s10969-012-9129-3
Vagin A, Teplyakov A (1997) MOLREP: an automated program for molecular replacement. J Appl Crystallogr 30:1022–1025
Zhou A, Carrell RW, Murphy MP, Wei Z, Yan Y, Stanley PLD, Stein PE, Broughton Pipkin F, Read RJ (2010) A redox switch in angiotensinogen modulates angiotensin release. Nature 468:108–111
Acknowledgments
Our work on Phaser is supported by awards from the Wellcome Trust (082961/Z/07/Z) and the NIH (Grant No. P01GM063210). We are grateful to users who provide us with bug reports and challenging problems that push the limits.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media Dordrecht
About this paper
Cite this paper
Read, R.J., McCoy, A.J., Oeffner, R.D., Bunkóczi, G. (2013). Extending the Reach of Molecular Replacement. In: Read, R., Urzhumtsev, A., Lunin, V. (eds) Advancing Methods for Biomolecular Crystallography. NATO Science for Peace and Security Series A: Chemistry and Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6232-9_11
Download citation
DOI: https://doi.org/10.1007/978-94-007-6232-9_11
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-007-6231-2
Online ISBN: 978-94-007-6232-9
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)