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Real-space refinement in PHENIX for cryo-EM and crystallography

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Afonine, Pavel V., Poon, Billy K., Read, Randy J., Sobolev, Oleg V., Terwilliger, Thomas C., Urzhumtsev, Alexandre, Adams, Paul D.·2018·Acta Crystallographica Section D Structural Biology
DOI 10.1107/s2059798318006551

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Abstract

This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.

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Show all 5 references

Research works printed but not linked: 79

  1. Afonine, 2009, J. Appl. Cryst., 42, 607, 10.1107/S0021889809023528 · DOI
  2. Afonine, 2018, bioRxiv. https://doi., org/101101/249607
  3. Afonine, P., Urzhumtsev, A. & Adams, P. D. (2015). Arbor, 191, a219. https://doi.org/10.3989/arbor.2015.772n2005. · DOI
  4. Ahmed, 2017, Nucleic Acids Res., 45, 8581, 10.1093/nar/gkx499 · DOI
  5. Ahmed, 2016, Sci Rep., 6, 35793, 10.1038/srep35793 · DOI
  6. Arnold, 1988, Acta Cryst. A, 44, 270, 10.1107/S0108767387011875 · DOI
  7. Baker, 2013, Proc. Natl Acad. Sci. USA, 110, 12301, 10.1073/pnas.1309947110 · DOI
  8. Barad, 2015, Nature Methods, 12, 943, 10.1038/nmeth.3541 · DOI · Paper page
  9. Berman, 2000, Nucleic Acids Res., 28, 235, 10.1093/nar/28.1.235 · DOI · Paper page
  10. Bernstein, 1977, J. Mol. Biol., 112, 535, 10.1016/S0022-2836(77)80200-3 · DOI · Paper page
  11. Bhardwaj, 2016, J. Biol. Chem., 291, 215, 10.1074/jbc.M115.696260 · DOI
  12. Brändén, 1990, Nature (London), 343, 687, 10.1038/343687a0 · DOI · Paper page
  13. Brown, 2015, Acta Cryst. D, 71, 136, 10.1107/S1399004714021683 · DOI
  14. Brünger, 1992, Nature (London), 355, 472, 10.1038/355472a0 · DOI
  15. Brünger, 1998, Acta Cryst. D, 54, 905, 10.1107/S0907444998003254 · DOI · Paper page
  16. Brünger, 1987, Science, 235, 458, 10.1126/science.235.4787.458 · DOI
  17. Chapman, 1995, Acta Cryst. A, 51, 69, 10.1107/S0108767394007130 · DOI
  18. Chen, 2009, Protein Sci., 18, 2403, 10.1002/pro.250 · DOI
  19. Chen, 2016, Science, 353, aad8266, 10.1126/science.aad8266 · DOI · Paper page
  20. Cheng, 2011, Proc. Natl Acad. Sci. USA, 108, 1373, 10.1073/pnas.1014995108 · DOI
  21. Chua, 2016, Nucleic Acids Res., 44, 8013, 10.1093/nar/gkw708 · DOI
  22. Demo, 2017, Elife, 6, e23687, 10.7554/eLife.23687 · DOI
  23. DiMaio, 2015, Nature Methods, 12, 361, 10.1038/nmeth.3286 · DOI
  24. Emsley, 2010, Acta Cryst. D, 66, 486, 10.1107/S0907444910007493 · DOI · Paper page
  25. Fischer, 2015, Nature (London), 520, 567, 10.1038/nature14275 · DOI · Paper page
  26. Frank, J. (2006). Three-Dimensional Electron Microscopy of Macromolecular Assemblies. Oxford University Press. · DOI · Paper page
  27. Gao, 2016, Nature (London), 534, 347, 10.1038/nature17964 · DOI · Paper page
  28. Goddard, 2018, Protein Sci., 27, 14, 10.1002/pro.3235 · DOI · Paper page
  29. Gore, 2017, Structure, 25, 1916, 10.1016/j.str.2017.10.009 · DOI
  30. Grosse-Kunstleve, 2002, J. Appl. Cryst., 35, 126, 10.1107/S0021889801017824 · DOI · Paper page
  31. Headd, 2012, Acta Cryst. D, 68, 381, 10.1107/S0907444911047834 · DOI · Paper page
  32. Headd, 2014, Acta Cryst. D, 70, 1346, 10.1107/S1399004714003277 · DOI
  33. Henderson, 2012, Structure, 20, 205, 10.1016/j.str.2011.12.014 · DOI · Paper page
  34. Henrick, 2003, J. Struct. Biol., 144, 228, 10.1016/j.jsb.2003.09.009 · DOI
  35. Hodel, 1992, Acta Cryst. A, 48, 851, 10.1107/S0108767392006044 · DOI
  36. Hryc, 2017, Proc. Natl Acad. Sci. USA, 114, 3103, 10.1073/pnas.1621152114 · DOI
  37. Jones, 1978, J. Appl. Cryst., 11, 268, 10.1107/S0021889878013308 · DOI
  38. Jones, 1991, Acta Cryst. A, 47, 110, 10.1107/S0108767390010224 · DOI · Paper page
  39. Joseph, 2017, J. Struct. Biol., 199, 12, 10.1016/j.jsb.2017.05.007 · DOI
  40. Kim, 2017, Biosci. Rep., 37, BSR20170072, 10.1042/BSR20170072 · DOI
  41. Lagerstedt, 2013, J. Struct. Biol., 184, 173, 10.1016/j.jsb.2013.09.021 · DOI
  42. Lekien, 2005, Int. J. Numer. Methods Eng., 63, 455, 10.1002/nme.1296 · DOI
  43. Leslie, 1987, Acta Cryst. A, 43, 134, 10.1107/S0108767387099720 · DOI
  44. Liao, 2013, Nature (London), 504, 107, 10.1038/nature12822 · DOI
  45. Liu, 1989, Math. Program., 45, 503, 10.1007/BF01589116 · DOI · Paper page
  46. Liu, 2017, J. Mol. Biol., 429, 1829, 10.1016/j.jmb.2017.05.011 · DOI
  47. Lokareddy, 2017, Nature Commun., 8, 14310, 10.1038/ncomms14310 · DOI
  48. Lunin, 2002, Acta Cryst. A, 58, 270, 10.1107/S0108767302001046 · DOI
  49. Lunin, 1984, Acta Cryst. A, 40, 269, 10.1107/S0108767384000544 · DOI
  50. Maslen, E. N., Fox, A. G. & O'Keefe, M. A. (1992). International Tables for Crystallography, Vol. C, edited by A. J. C. Wilson, pp. 476-516. Dordrecht: Kluwer Academic Publishers.
  51. Mooij, 2006, ChemMedChem, 1, 827, 10.1002/cmdc.200600074 · DOI
  52. Oldfield, 2001, Acta Cryst. D, 57, 82, 10.1107/S0907444900014098 · DOI
  53. Paulino, 2017, Elife, 6, e26232, 10.7554/eLife.26232 · DOI
  54. Peng, 1998, Acta Cryst. A, 54, 481, 10.1107/S0108767398001901 · DOI
  55. Peng, 1996, Acta Cryst. A, 52, 257, 10.1107/S0108767395014371 · DOI
  56. Pintilie, 2016, Biophys. J., 110, 827, 10.1016/j.bpj.2015.11.3522 · DOI
  57. Read, 1986, Acta Cryst. A, 42, 140, 10.1107/S0108767386099622 · DOI · Paper page
  58. Read, 2011, Structure, 19, 1395, 10.1016/j.str.2011.08.006 · DOI
  59. Rossmann, 2000, Acta Cryst. D, 56, 1341, 10.1107/S0907444900009562 · DOI
  60. Rossmann, 2001, J. Struct. Biol., 136, 190, 10.1006/jsbi.2002.4435 · DOI
  61. Sears, 1992, Neutron News, 3(3), 26, 10.1080/10448639208218770 · DOI
  62. Shalev-Benami, 2016, Cell. Rep., 16, 288, 10.1016/j.celrep.2016.06.014 · DOI
  63. Sheldrick, 1997, Methods Enzymol., 277, 319, 10.1016/S0076-6879(97)77018-6 · DOI
  64. Sobolev, 2015, J. Appl. Cryst., 48, 1130, 10.1107/S1600576715010432 · DOI
  65. Sorzano, 2015, AIMS Biophys., 2, 8, 10.3934/biophy.2015.1.8 · DOI
  66. Terwilliger, T. C., Adams, P. D., Afonine, P. V. & Sobolev, O. V. (2018). bioRxiv, 267138. https://doi.org/10.1101/267138. · DOI
  67. Terwilliger, 2007, Acta Cryst. D, 63, 597, 10.1107/S0907444907009791 · DOI
  68. Terwilliger, 2013, Acta Cryst. D, 69, 2244, 10.1107/S0907444913017770 · DOI
  69. Terwilliger, 2018, Acta Cryst. D, 74, 545, 10.1107/S2059798318004655 · DOI
  70. Tickle, 2012, Acta Cryst. D, 68, 454, 10.1107/S0907444911035918 · DOI
  71. Tronrud, 2004, Acta Cryst. D, 60, 2156, 10.1107/S090744490402356X · DOI
  72. Turk, 2013, Acta Cryst. D, 69, 1342, 10.1107/S0907444913008408 · DOI
  73. Urzhumtsev, 2014, Acta Cryst. D, 70, 2593, 10.1107/S1399004714016289 · DOI
  74. Urzhumtsev, 1989, Acta Cryst. A, 45, 34, 10.1107/S0108767388008955 · DOI
  75. Waasmaier, 1995, Acta Cryst. A, 51, 416, 10.1107/S0108767394013292 · DOI
  76. Watkin, 2008, J. Appl. Cryst., 41, 491, 10.1107/S0021889808007279 · DOI
  77. Williams, 2018, Protein Sci., 27, 193, 10.1002/pro.3330 · DOI · Paper page
  78. Wlodawer, 2017, Acta Cryst. D, 73, 379, 10.1107/S205979831700225X · DOI
  79. Yang, 2016, Protein Cell, 7, 878, 10.1007/s13238-016-0346-6 · DOI · Paper page

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Items 101–200 of 209

Metadata

Authors
Afonine, P. V., Poon, B. K., Read, R. J., Sobolev, O. V., Terwilliger, T. C., Urzhumtsev, A., & Adams, P. D.
Venue
Acta Crystallographica Section D Structural Biology
Publisher
International Union of Crystallography (IUCr)
Published
2018-05-30
Volume
74
Issue
6
Pages
531-544
ISSN
2059-7983 (ISSN-L)
DOI
10.1107/s2059798318006551
OpenAlex
W2786390877
Cited by
3,281
References
5
FWCI
68.86
Type
journal article
Language
en
Open access
hybrid
Licence
Funders
  • National Institutes of Health (GM063210)
  • PHENIX Industrial Consortium
  • U.S. Department of Energy (DE-AC02-05CH11231)
  • French Infrastructure for Integrated Structural Biology (ANR-10-INBS-05)
  • Wellcome Trust (082961/ Z/07/Z)

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