Experimental phasing with SHELXC/D/E: combining chain tracing with density modification.
The programs SHELXC, SHELXD and SHELXE are designed to provide simple, robust and efficient experimental phasing of macromolecules by the SAD, MAD, SIR, SIRAS and RIP methods and are particularly suitable for use in automated structure-solution pipelines. This paper gives a general account of experimental phasing using these programs and describes the extension of iterative density modification in SHELXE by the inclusion of automated protein main-chain tracing. This gives a good indication as to whether the structure has been solved and enables interpretable maps to be obtained from poorer starting phases. The autotracing algorithm starts with the location of possible seven-residue alpha-helices and common tripeptides. After extension of these fragments in both directions, various criteria are used to decide whether to accept or reject the resulting poly-Ala traces. Noncrystallographic symmetry (NCS) is applied to the traced fragments, not to the density. Further features are the use of a 'no-go' map to prevent the traces from passing through heavy atoms or symmetry elements and a splicing technique to combine the best parts of traces (including those generated by NCS) that partly overlap.
Sheldrick
George M
GM
Department of Structural Chemistry, University of Göttingen, Tammannstrasse 4, D-37077 Göttingen, Germany. gsheldr@shelx.uni-ac.gwdg.de
D000465:Algorithms; D018360:Crystallography, X-Ray / Q000379:methods*; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000032:analysis / Q000737:chemistry
D011506:Proteins
Methods Enzymol. 1985;115:41-55
4079795
Structure. 1997 Dec 15;5(12):1557-69
9438862
Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):449-57
15805600
Acta Crystallogr D Biol Crystallogr. 1997 Mar 1;53(Pt 2):179-85
15299952
Acta Crystallogr D Biol Crystallogr. 2005 Nov;61(Pt 11):1465-75
16239723
Acta Crystallogr D Biol Crystallogr. 2000 Aug;56(Pt 8):965-72
10944333
Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1002-11
16929101
Acta Crystallogr D Biol Crystallogr. 2009 Oct;65(Pt 10):1089-97
19770506
Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):38-44
12499537
Acta Crystallogr D Biol Crystallogr. 2007 Nov;63(Pt 11):1162-8
18007031
Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1227-37
16131756
Acta Crystallogr A. 2008 Jan;64(Pt 1):112-22
18156677
J Mol Biol. 2001 Mar 2;306(4):759-71
11243786
Nat Struct Biol. 1999 May;6(5):458-63
10331874
J Struct Biol. 2009 Jan;165(1):47-52
18952182
Acta Crystallogr D Biol Crystallogr. 2003 Oct;59(Pt 10):1688-701
14501107
Acta Crystallogr D Biol Crystallogr. 1998 Jul 1;54(Pt 4):487-93
9761844
Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):556-65
15858265
Acta Crystallogr D Biol Crystallogr. 1997 Jul 1;53(Pt 4):371-6
15299902
Acta Crystallogr D Biol Crystallogr. 2000 Dec;56(Pt 12):1612-21
11092927
Acta Crystallogr D Biol Crystallogr. 2007 Oct;63(Pt 10):1069-74
17881824
Acta Crystallogr D Biol Crystallogr. 2003 Dec;59(Pt 12):2125-32
14646070
Acta Crystallogr D Biol Crystallogr. 2002 Oct;58(Pt 10 Pt 2):1772-9
12351820
Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1941-7
12393926
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
15572765
Curr Opin Struct Biol. 1999 Oct;9(5):643-8
10508770
Acta Crystallogr D Biol Crystallogr. 2006 Nov;62(Pt 11):1401-6
17057345
J Mol Biol. 2007 May 4;368(3):833-44
17368672
Methods Enzymol. 1985;115:90-112
4079800