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Crystallographic Maps and Models at Low and at Subatomic Resolutions

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Advancing Methods for Biomolecular Crystallography

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Abstract

Crystallographic studies at both extremes of the resolution interval, low and subatomic, are less common in macromolecular crystallography and have their own specific features. Ignoring these features may complicate structure solution or lead to errors in crystallographic Fourier maps and in their interpretation.

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References

  1. 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

    Article  Google Scholar 

  2. Aevarsson A, Brazhnikov E, Garber M, Zheltonosova J, Chirgadze Y, Al-Karadaghi S, Svensson LA, Lilias A (1994) Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. EMBO J 13:3669–3677

    CAS  Google Scholar 

  3. Afonine PV, Lunin VY, Muzet N, Urzhumtsev A (2004) On the possibility of observation of valence electron density for individual bonds in proteins in conventional difference maps. Acta Crystallogr D 60:260–274

    Article  Google Scholar 

  4. Afonine PV, Grosse-Kunstleve RW, Adams PD, Lunin VY, Urzhumtsev A (2007) On macromolecular refinement at subatomic resolution with interatomic scatterers. Acta Crystallogr D 63:1194–1197

    Article  Google Scholar 

  5. Afonine PV, Mustyakimov M, Grosse-Kunstleve RW, Moriarty NW, Langan P, Adams PD (2010) Joint X-ray and neutron refinement with phenix.refine. Acta Crystallogr D 66:1153–1163

    Article  Google Scholar 

  6. Ban N, Freeborn B, Nissen P, Penczek P, Grassucci RA, Sweet R, Frank J, Moore PB, Steitz TA (1998) A 9 Å resolution X-ray crystallographic map of the large ribosomal subunit. Cell 93:1105–1115

    Article  CAS  Google Scholar 

  7. Bentley GA, Lewit-Bentley A, Finch JT, Podjarny AD, Roth M (1984) Crystal structure of the nucleosome core particle at 16 A resolution. J Molec Biol 176:55–75

    Article  CAS  Google Scholar 

  8. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235–242

    Article  CAS  Google Scholar 

  9. Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977) The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 112:535–542

    Article  CAS  Google Scholar 

  10. Bochow A, Urzhumtsev A (2005) On the Fourier series truncation peaks at subatomic resolution. CCP4 Newsletter on Protein Crystallography 42: http://www.ccp4.ac.uk/newsletters/newsletter42/content.html

  11. Chang G, Roth CB, Reyes CL, Pornillos O, Chen YJ, Chen AP (2006) Retraction. Science 314:1875

    Article  CAS  Google Scholar 

  12. Chirgadze YN, Brazhnikov EV, Garber MB, Nikonov SV, Fomenkova NP, Lunin VY, Urzhumtsev A, Chirgadze NY, Nekrasov YV (1991) Crystal structure of ribosomal factor G from bacteria Thermus thermophilus at low resolution. Dokl Acad Nauk SSSR 320:488–491

    CAS  Google Scholar 

  13. DeLano WL (2002) The PyMOL Molecular Graphics System, DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org

  14. Dittrich B, Hübschle CB, Messerschmidt M, Kalinowski R, Girnt D, Luger P (2005) The invariome model and its application: refinement of D, L-serine at different temperatures and resolution. Acta Crystallogr A 61:314–320

    Article  CAS  Google Scholar 

  15. Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of coot. Acta Crystallogr D 66:486–501

    Article  CAS  Google Scholar 

  16. Fenn TD, Schnieders MJ, Brunger AT (2010) A smooth and differentiable bulk-solvent model for macromolecular diffraction. Acta Crystallogr D 66:1024–1031

    Article  CAS  Google Scholar 

  17. Hansen NK, Coppens P (1978) Testing aspherical atom refinements on small-molecule data sets. Acta Crystallogr A 34:909–921

    Article  Google Scholar 

  18. Jelsch C, Pichon-Pesme V, Lecomte C, Aubry A (1998) Acta Crystallogr D 54:1306–1318

    Article  CAS  Google Scholar 

  19. Jiang JS, Brünger AT (1994) Protein hydration observed by X-ray diffrcation. Solvation properties of penicillopepsin and neuraminidase crystal structures. J Mol Biol 243:100–115

    Article  CAS  Google Scholar 

  20. Johnson JE, Akimoto T, Suck D, Rayment I, Rossmann MG (1976) The structure of southern bean mosaic virus at 22.5 resolution. Virology 75:394–400

    Article  CAS  Google Scholar 

  21. Kalinin DI (1980) Use of a cylindrical model of a protein to determine the spatial structure of the rhombic modification of leghaemoglobin. Sov Phys Crystallogr 25:307–313

    Google Scholar 

  22. Ko TP, Robinson H, Gao YG, Cheng CHC, DeVries AL, Wang AHJ (2003) The refined crystal structure of an Eel pout type III antifreeze protein RD1 at 0.62-A resolution reveals structural microheterogeneity of protein and solvation. Biophys J 84:1228–1237

    Article  CAS  Google Scholar 

  23. Lunin VY (1988) Use of information on electron density distribution in macromolecules. Acta Crystallogr A 44:144–150

    Article  Google Scholar 

  24. Lunin VY, Lunina NL, Petrova TE, Vernoslova EA, Urzhumtsev A, Podjarny AD (1995) On the ab initio solution of the phase problem for macromolecules at very low resolution: the Few Atoms Model method. Acta Crystallogr D 51:896–903

    Article  CAS  Google Scholar 

  25. Lunin VY, Lunina N, Urzhumtsev A (1999) Seminvariant density decomposition and connectivity analysis in very low resolution macromolecular phasing. Acta Crystallogr A 55:916–925

    Article  Google Scholar 

  26. Lunin VY, Lunina N, Ritter S, Frey I, Keul J, Diederichs K, Podjarny A, Urzhumtsev A, Baumstark M (2001) Low-resolution data analysis for the low-density lipoprotein particle. Acta Crystallogr D 57:108–121

    Article  CAS  Google Scholar 

  27. Lunin VY, Urzhumtsev A, Bockmayr A (2002) Direct phasing by binary integer programming. Acta Crystallogr A 58:283–291

    Article  Google Scholar 

  28. Lunin VY, Urzhumtsev A, Podjarny AD (2012) An initio phasing of low-resolution Fourier syntheses. In: Himmel DM, Rossmann MG, Arnold E (eds) International tables for crystallography, vol F. Wiley, Chichester, pp 437–442

    Chapter  Google Scholar 

  29. Phillips SEV (1980) Structure and refinement of oxymyoglobin at 1.6 Å resolution. J Mol Biol 142:531–554

    Article  CAS  Google Scholar 

  30. Pichon-Pesme V, Lachekar H, Souhassou M, Lecomte C (2000) Electron density and electrostatic properties of two peptide molecules: tyrosyl-glycyl-glycyne monohydrate and glycyl-aspartic acid dehydrate. Acta Crystallogr B 56:728–737

    Article  CAS  Google Scholar 

  31. Podjarny AD, Rees B, Thierry JC, Cavarelli J, Jesior JC, Roth M, Lewitt-Bentley A, Kahn R, Lorber B, Ebel JP, Giegé R, Moras D (1987) Yeast tRNAAsp –aspartyl-tRNA synthetase complex: low resolution crystal structure. J Biomol Struct Dyn 5:187–198

    Article  CAS  Google Scholar 

  32. Schnieders MJ, Fenn TD, Pande VS, Brunger AT (2009) Polarizable atomic multipole X-ray refinement: application to peptide crystals. Acta Crystallogr D 65:952–965

    Article  Google Scholar 

  33. Strop P, Brzustowicz MR, Brunger AT (2007) Ab initio molecular-replacement phasing for symmetric helical membrane proteins. Acta Crystallogr D 63:188–196

    Article  Google Scholar 

  34. Svergun DI, Petoukhov MV, Koch MHJ (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys J 80:2946–2953

    Article  CAS  Google Scholar 

  35. Urzhumtsev A (1991) Low-resolution phases: their influence on SIR-syntheses and retrieval with double-step-filtration. Acta Crystallogr A 47:794–801

    Article  Google Scholar 

  36. Urzhumtsev A, Podjarny AD (1995) On the solution of the molecular-replacement problem at very low resolution: application to large complexes. Acta Crystallogr D 51:888–895

    Article  CAS  Google Scholar 

  37. Urzhumtsev A, Podjarny AD (1995) On the problem of solvent modelling in macromolecular crystals using diffractional data: 1. The low resolution range. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31: 12–16

    Google Scholar 

  38. Urzhumtsev A, Afonine PV, Adams PD (2009) On the use of logarithmic scales for analysis of diffraction data. Acta Crystallogr D 65:1283–1291

    Article  Google Scholar 

  39. Volkov A, Messerschmidt M, Coppens P (2007) Improving the scattering-factor formalism in protein refinement: application of the University at Buffalo Aspherical-Atom Databank to polypeptide structures. Acta Crystallogr D 63:160–170

    Article  Google Scholar 

  40. von Castelmur E, Marino M, Svergun DI, Kreplak L, Labeit D, Ucurum-Fotiadis Z, Konarev PV, Urzhumtsev A, Labeit S, Mayans O (2007) A regular pattern of Ig super-motifs defines segmental flexibility as the elastic mechanism of the titin chain. Proc Natl Acad Sci 105:1186–1191

    Article  Google Scholar 

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Acknowledgment

VL thanks RFBR 10-04-00254-a grant for financial support. PA acknowledges the NIH (grant GH063210) and the Phenix Industrial Consortium for support of the Phenix project. PyMol [13] and coot [15] were used for illustrations. The authors thank all persons contributed to different parts of the relevant projects and A. McEwen for careful reading and correcting the text

Author information

Authors and Affiliations

  1. IGBMC, CNRS-INSERM-UdS, 1 rue Laurent Fries, 10142, 67404, Illkirch, France

    Alexandre G. Urzhumtsev

  2. Physics Department, Faculté des Sciences et des Technologies, Université de Lorraine, 239, 54506, Vandoeuvre-lès-Nancy, France

    Alexandre G. Urzhumtsev

  3. Lawrence Berkeley National Laboratory, One Cyclotron Road, BLDG 64R0121, Berkeley, CA, 94720, USA

    Pavel V. Afonine

  4. Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, 142290, Russia

    Vladimir Y. Lunin

Authors
  1. Alexandre G. Urzhumtsev
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  2. Pavel V. Afonine
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  3. Vladimir Y. Lunin
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Corresponding author

Correspondence to Alexandre G. Urzhumtsev .

Editor information

Editors and Affiliations

  1. , Department of Haematology, University of Cambridge, Hills Road, Cambridge, CB2 0XY, United Kingdom

    Randy Read

  2. Fac.des Sciences et des Technologies, Physics Department, Université de Lorraine, Blvd. des Aiguillettes 1, Vandoeuvre-lès-Nancy, 54506, France

    Alexandre G. Urzhumtsev

  3. , Institute of Mathematical Problems of Bi, Russian Academy of Sciences, Institutskaya st. 4, Pushchino, 142290, Russia

    Vladimir Y. Lunin

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Urzhumtsev, A.G., Afonine, P.V., Lunin, V.Y. (2013). Crystallographic Maps and Models at Low and at Subatomic Resolutions. 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_21

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