Advanced crystallographic data collection protocols for experimental phasing

Methods in Molecular Biology

Volumn 1320, Issue , 2016, Pages 175-191

  Finke, Aaron D ^a   Panepucci, Ezequiel ^a   Vonrhein, Clemens ^a   Wang, Meitian ^a   Bricogne, Gérard ^a   Oliéric, Vincent ^a  

^a NONE

Author keywords

Anomalous scattering; Diffraction data collection; Experimental phasing; Macromolecular crystallography; Multi axis goniometry; strategies

Indexed keywords

ARTICLE; COMPUTER INTERFACE; CONTROLLED STUDY; CRYSTAL; CRYSTALLOGRAPHY; DATA ANALYSIS SOFTWARE; DECISION MAKING; DISPERSION; GONIOMETER; GONIOMETRY; INFORMATION PROCESSING; LOW TEMPERATURE; MULTI WAVELENGTH ANOMALOUS DISPERSION; PRIORITY JOURNAL; RADIATION INJURY; SIGNAL NOISE RATIO; SINGLE WAVELENGTH ANOMALOUS DISPERSION; SYNCHROTRON; X RAY ABSORPTION SPECTROSCOPY; X RAY DETECTOR; X RAY FLUORESCENCE;

DATA HANDLING; DECISION MAKING; INSTRUMENT ERRORS; MACROMOLECULES; RADIATION DAMAGE;

ANOMALOUS SCATTERING; DIFFRACTION DATA; EXPERIMENTAL PHASING; MACROMOLECULAR CRYSTALLOGRAPHY; MULTI-AXIS;

DATA ACQUISITION;

EID: 84938337146     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-2763-0_11     Document Type: Article

References (49)

1. Hendrickson WA (2013) Evolution of diffraction methods for solving crystal structures. Acta Crystallogr A 69:51-59
2. Hendrickson WA (2014) Anomalous diffraction in crystallographic phase evaluation. Q Rev Biophys 47:49-93
3. Hendrickson WA, Horton JR, LeMaster DM (1990) Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J 9:1665-1672
4. Doublié S (1997) Preparation of selenomethionyl proteins for phase determination. Methods Enzymol 276:523-530
5. Dauter Z (2010) Carrying out an optimal experiment. Acta Crystallogr D 66:389-392
6. Ennifar E, Walter P, Dumas P (2003) A crystallographic study of the binding of 13 metal ions to two related RNA duplexes. Nucleic Acids Res 31:2671-2682
7. Keel AY, Rambo RP, Batey RT, Kieft J (2007) A general strategy to solve the phase problem in RNA crystallography. Structure 15:761-772
8. Henderson R (1990) Cryoprotection of protein crystals against radiation-damage in electron and X-ray diffraction. Proc R Soc B Biol Sci 241:6-8
9. Hendrickson WA, Teeter MM (1981) Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulphur. Nature 290:107-113
10. Kahn R, Fourme R, Bosshard R, Chiadmi M, Risler JL, Dideberg O, Wery JP (1985) Crystal structure study of Opsanus tau parvalbumin by multiwavelength anomalous diffraction. FEBS Lett 179:133-137
11. Hendrickson WA, Pähler A, Smith JL, Satow Y, Merritt EA, Phizackerley RP (1989) Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. Proc Natl Acad Sci U S A 86:2190-2194
12. Weis WI, Kahn R, Fourme R, Drickamer K, Hendrickson WA (1991) Structure of the calcium- dependent lectin domain from a rat mannose-binding protein determined by MAD phasing. Science 254:1608-1615
13. Hendrickson WA, Ogata C (1997) Phase determination from multiwavelength anomalous diffraction measurements. Methods Enzymol 276:494-523
14. Rupp B (2009) Biomolecular crystallography: principles, practice, and application to structural biology. Garland Science, New York
15. Legrand P. xdsme. http://code.google.com/ p/xdsme/
16. Broennimann C, Eikenberry EF, Henrich B, Horisberger R, Huelsen G, Pohl E, Schmitt B, Schulze-Briese C, Suzuki M, Tomizaki T, Toyokawa H, Wagner A (2006) The PILATUS 1M detector. J Synchrotron Radiat 13:120-130
17. Walsh MA, Dementieva I, Evans G, Sanishvili R, Joachimiak A (1999) Taking MAD to the extreme: ultrafast protein structure determination. Acta Crystallogr D 55:1168-1173
18. Rice LM, Earnest TN, Brunger AT (2000) Single-wavelength anomalous diffraction phasing revisited. Acta Crystallogr D 56:1413-1420
19. Clemons WM, Brodersen DE, McCutcheon JP, May JL, Carter AP, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V (2001) Crystal structure of the 30S ribosomal subunit from Thermus thermophilus: purifi cation, crystallization and structure determination. J Mol Biol 310:827-843
20. Voss JE, Vaney M-C, Duquerroy S, Vonrhein C, Girard-Blanc C, Crublet E, Thompson A, Bricogne G, Rey FA (2010) Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography. Nature 468:709-712
21. Liu Q, Dahmane T, Zhang Z, Assur Z, Brasch J, Shapiro L, Mancia F, Hendrickson WA (2012) Structures from anomalous diffraction of native biological macromolecules. Science 336:1033-1037
22. Weinert T, Olieric V, Waltersperger S, Panepucci E, Chen L, Zhang H, Zhou D, Rose J, Ebihara A, Kuramitsu S, Li D, Howe N, Schnapp G, Pautsch A, Bargsten K, Prota AE, Surana P, Kottur J, Nair DT, Basolico F, Cecatiello V, Pasqualato S, Boland A, Weichenrieder O, Wang BC, Steinmetz MO, Caffrey M, Wang M (2014) Fast native-SAD phasing for routine macromolecular structure determination. Nat Methods 12(2):131-133
23. Dauter Z (2002) New approaches to highthroughput phasing. Curr Opin Struct Biol 12:674-678
24. Brockhauser S, Ravelli RBG, McCarthy AA (2013) The use of a mini-κ goniometer head in macromolecular crystallography diffraction experiments. Acta Crystallogr D 69:1241-1251
25. Waltersperger S, Olieric V, Pradervand C, Glettig W, Salathe M, Fuchs MR, Curtin A, Wang X, Ebner S, Panepucci E, Weinert T, Schulze-Briese C, Wang M (2015) PRIGo: a new multi-axis goniometer for macromolecular crystallography. J Synchrotron Radiat In Press
26. Alkire RW, Duke NEC, Rotella FJ (2008) Is your cold-stream working for you or against you ? An in-depth look at temperature and sample motion research papers. J Appl Crystallogr 41:1122-1133
27. Mueller M, Wang M, Schulze-Briese C (2012) Optimal fi ne φ-slicing for single-photoncounting pixel detectors. Acta Crystallogr D 68:42-56
28. Evans G, Pettifer R (2001) CHOOCH: a program for deriving anomalous-scattering factors from X-ray fl uorescence spectra. J Appl Crystallogr 34:82-86
29. Kabsch W (2010) XDS. Acta Crystallogr D 66:125-132
30. Leslie A, Powell H (2007) Processing diffraction data with Mosfl m. Evol Meth Macromol Crystallogr NATO Sci II Math Phys Chem 245:41-51
31. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data. Meth Enzymol 276: 307-326
32. Vonrhein C, Flensburg C, Keller P, Sharff A, Smart O, Paciorek W, Womack T, Bricogne G (2011) Data processing and analysis with the autoPROC toolbox. Acta Crystallogr D 67: 293-302
33. Winter G, Lobley CMC, Prince SM (2013) Decision making in xia2. Acta Crystallogr D 69:1260-1273
34. Diederichs K, McSweeney S, Ravelli RBG (2003) Zero-dose extrapolation as part of macromolecular synchrotron data reduction. Acta Crystallogr D 59:903-909
35. Sheldrick GM (2010) Experimental phasing with SHELXC/D/E: combining chain tracing with density modifi cation. Acta Crystallogr D 66:479-485
36. Pape T, Schneider TR (2004) HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programs. J Appl Crystallogr 37:843-844
37. Vonrhein C, Blanc E, Roversi P, Bricogne G (2007) Automated structure solution with autoSHARP. Methods Mol Biol 364: 215-230
38. Terwilliger TC, Adams PD, Read RJ, McCoy AJ, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW (2009) Decisionmaking in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta Crystallogr D 65:582-601
39. Skubák P, Pannu NS (2013) Automatic protein structure solution from weak X-ray data. Nat Commun 4:2777
40. Dauter Z, Adamiak DA (2001) Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy. Acta Crystallogr D 57:990-995
41. Luo Z, Dauter M, Dauter Z (2014) Phosphates in the Z-DNA dodecamer are fl exible, but their P-SAD signal is suffi cient for structure solution. Acta Crystallogr D 70:1790-1800
42. Liu Q, Guo Y, Chang Y, Cai Z, Assur Z, Mancia F, Greene MI, Hendrickson WA (2014) Multi-crystal native SAD analysis at 6 keV. Acta Crystallogr D 70:2544-2557
43. Liu Q, Liu Q, Hendrickson WA (2013) Robust structural analysis of native biological macromolecules from multi-crystal anomalous diffraction data. Acta Crystallogr D 69:1314-1332
44. González A (2003) Optimizing data collection for structure determination. Acta Crystallogr D 59:1935-1942
45. Liu Q, Zhang Z, Hendrickson WA (2011) Multi-crystal anomalous diffraction for lowresolution macromolecular phasing. Acta Crystallogr D 67:45-59
46. González A, Pédelacq J, Solà M, Gomis-Rüth FX, Coll M, Samama J, Benini S (1999) Twowavelength MAD phasing: in search of the optimal choice of wavelengths. Acta Crystallogr D 55:1449-1458
47. Diederichs K (2010) Quantifying instrument errors in macromolecular X-ray data sets. Acta Crystallogr D 66:733-740
48. Holton JM (2009) A beginner's guide to radiation damage. J Synchrotron Radiat 16:133-142
49. Zeldin OB, Gerstel M, Garman EF (2013) RADDOSE-3D: time- and space-resolved modelling of dose in macromolecular crystallography. J Appl Crystallogr 46:1225-1230