journal article·2015-07-01Open access

Native SAD is maturing

John P. Rose, Bi-Cheng Wang, Manfred S. Weiss

IUCrJ· Volume 2· Issue 4

Abstract

Native SAD phasing uses the anomalous scattering signal of light atoms in the crystalline, native samples of macromolecules collected from single-wavelength X-ray diffraction experiments. These atoms include sodium, magnesium, phosphorus, sulfur, chlorine, potassium and calcium. Native SAD phasing is challenging and is critically dependent on the collection of accurate data. Over the past five years, advances in diffraction hardware, crystallographic software, data-collection methods and strategies, and the use of data statistics have been witnessed which allow `highly accurate data' to be routinely collected. Today, native SAD sits on the verge of becoming a `first-choice' method for bothde novoand molecular-replacement structure determination. This article will focus on advances that have caught the attention of the community over the past five years. It will also highlight bothde novonative SAD structures and recent structures that were key to methods development.
Source: crossref · Quality: baseline

Research context

OpenAlex topics: Enzyme Structure and Function · X-ray Diffraction in Crystallography · Iron oxide chemistry and applications

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

References (64)

Show source-provided references
1. Adams · Acta Cryst. D · 2010 · 66 · 21310.1107/S0907444909052925 ↗
2. Adams · Acc. Chem. Res. · 2003 · 36 · 19110.1021/ar0101382 ↗
3. Akey · Science · 2014 · 343 · 88110.1126/science.1247749 ↗
4. Alkire · J. Appl. Cryst. · 2008 · 41 · 112210.1107/S0021889808032536 ↗
5. Alkire · J. Appl. Cryst. · 2013 · 46 · 52510.1107/S0021889813003348 ↗
6. Berman · Nucleic Acids Res. · 2000 · 28 · 23510.1093/nar/28.1.235 ↗
7. Brockhauser · Acta Cryst. D · 2013 · 69 · 124110.1107/S0907444913003880 ↗
8. Broennimann · J. Synchrotron Rad. · 2006 · 13 · 12010.1107/S0909049505038665 ↗
9. Bunkóczi · Nature Methods · 2014 · 12 · 12710.1038/nmeth.3212 ↗
10. Chen · Proc. Natl Acad. Sci. USA · 1991 · 88 · 424010.1073/pnas.88.10.4240 ↗
11. Chen · Acta Cryst. D · 2014 · 70 · 233110.1107/S1399004714013868 ↗
12. Chen · Am. Crystallogr. Assoc. Newsl. · 2000 · 3 · 28
13. Cianci · Acta Cryst. D · 2008 · 64 · 119610.1107/S0907444908030503 ↗
14. Cowtan · Acta Cryst. D · 2006 · 62 · 100210.1107/S0907444906022116 ↗
15. Dauter · J. Mol. Biol. · 1999 · 289 · 8310.1006/jmbi.1999.2743 ↗
16. Diederichs · Nature Struct. Mol. Biol. · 1997 · 4 · 26910.1038/nsb0497-269 ↗
17. El Omari · Acta Cryst. D · 2014 · 70 · 219710.1107/S139900471401339X ↗
18. Englich · J. Synchrotron Rad. · 2011 · 18 · 7010.1107/S0909049510036010 ↗
19. Flot · J. Synchrotron Rad. · 2010 · 17 · 10710.1107/S0909049509041168 ↗
20. Foadi · Acta Cryst. D · 2013 · 69 · 161710.1107/S0907444913012274 ↗
21. Garman, E. F. (2013). Advancing Methods for Biomolecular Crystallography, edited by R. Read, A. G. Urzhumtsev & V. Y. Lunin, pp. 69-77. Dordrecht: Springer.10.1007/978-94-007-6232-9_7 ↗
22. Henderson · Proc. R. Soc. B Biol. Sci. · 1990 · 241 · 610.1098/rspb.1990.0057 ↗
23. Hendrickson · Proc. Natl Acad. Sci. USA · 1989 · 86 · 219010.1073/pnas.86.7.2190 ↗
24. Hendrickson · Nature (London) · 1981 · 290 · 10710.1038/290107a0 ↗
25. Hilgart · J. Synchrotron Rad. · 2011 · 18 · 71710.1107/S0909049511029918 ↗
26. Kabsch · Acta Cryst. D · 2010 · 66 · 12510.1107/S0907444909047337 ↗
27. Kim · Acta Cryst. D · 2007 · 63 · 65310.1107/S0907444907011924 ↗
28. Kim · Acta Cryst. D · 2005 · 61 · 88110.1107/S090744490500836X ↗
29. Kitago · J. Appl. Cryst. · 2010 · 43 · 34110.1107/S0021889809054272 ↗
30. Kitamura · J. Biol. Chem. · 2008 · 283 · 3632810.1074/jbc.M806115200 ↗
31. Leslie, A. G. W. & Powell, H. R. (2007). Evolving Methods for Macromolecular Crystallography, edited by R. J. Read & J. L. Sussman, pp. 41-51. Dordrecht: Springer.10.1007/978-1-4020-6316-9_4 ↗
32. Liu · Acta Cryst. A · 2011 · 67 · 54410.1107/S0108767311037469 ↗
33. Liu · Science · 2012 · 336 · 103310.1126/science.1218753 ↗
34. Liu · Acta Cryst. D · 2013 · 69 · 131410.1107/S0907444913001479 ↗
35. Liu · Protein Sci. · 2000 · 9 · 208510.1110/ps.9.11.2085 ↗
36. Marchal · Nucl. Instrum. Methods Phys. Res. A · 2011 · 633 · S12110.1016/j.nima.2010.06.142 ↗
37. Minor · Acta Cryst. D · 2006 · 62 · 85910.1107/S0907444906019949 ↗
38. Monaco · J. Appl. Cryst. · 2013 · 46 · 80410.1107/S0021889813006195 ↗
39. Moore · Structure · 2012 · 20 · 72910.1016/j.str.2012.02.021 ↗
40. Mueller-Dieckmann · Acta Cryst. D · 2007 · 63 · 36610.1107/S0907444906055624 ↗
41. Mueller-Dieckmann · Acta Cryst. D · 2005 · 61 · 126310.1107/S0907444905021475 ↗
42. Müller · Acta Cryst. D · 2011 · 67 · 93610.1107/S0907444911037796 ↗
43. Mykhaylyk · J. Phys. Conf. Ser. · 2013 · 425 · 01201010.1088/1742-6596/425/1/012010 ↗
44. Otwinowski · Methods Enzymol. · 1997 · 276 · 30710.1016/S0076-6879(97)76066-X ↗
45. Owen · Proc. Natl Acad. Sci. USA · 2006 · 103 · 491210.1073/pnas.0600973103 ↗
46. Panjikar · Acta Cryst. D · 2005 · 61 · 44910.1107/S0907444905001307 ↗
47. Perrakis · Acta Cryst. D · 1999 · 55 · 176510.1107/S0907444999009348 ↗
48. Qi · Nature Struct. Mol. Biol. · 2013 · 20 · 90010.1038/nsmb.2583 ↗
49. Read · Acta Cryst. D · 2011 · 67 · 33810.1107/S0907444910051371 ↗
50. Rose · Rigaku J. · 2004 · 21 · 1
51. Ru · Acta Cryst. D · 2012 · 68 · 52110.1107/S0907444912004490 ↗
52. Sheldrick · Acta Cryst. D · 2010 · 66 · 47910.1107/S0907444909038360 ↗
53. Sugahara · PLoS One · 2014 · 9 · e9501710.1371/journal.pone.0095017 ↗
54. Teng · J. Appl. Cryst. · 1990 · 23 · 38710.1107/S0021889890005568 ↗
55. Thomanek · Acta Cryst. A · 1973 · 29 · 26310.1107/S0567739473000677 ↗
56. Wang · Methods Enzymol. · 1985 · 115 · 9010.1016/0076-6879(85)15009-3 ↗
57. Watanabe · Acta Cryst. D · 2006 · 62 · 89110.1107/S0907444906010432 ↗
58. Weinert · Nature Methods · 2015 · 12 · 13110.1038/nmeth.3211 ↗
59. Weiss · J. Appl. Cryst. · 2001 · 34 · 13010.1107/S0021889800018227 ↗
60. Wierman · J. Appl. Cryst. · 2013 · 46 · 150110.1107/S002188981301786X ↗
61. Winn · Acta Cryst. D · 2011 · 67 · 23510.1107/S0907444910045749 ↗
62. Yakunin · Curr. Opin. Chem. Biol. · 2004 · 8 · 4210.1016/j.cbpa.2003.12.003 ↗
63. Zeldin · Proc. Natl Acad. Sci. USA · 2013 · 110 · 2055110.1073/pnas.1315879110 ↗
64. Zeldin · J. Synchrotron Rad. · 2013 · 20 · 4910.1107/S0909049512044706 ↗