Access the full text.
Sign up today, get DeepDyve free for 14 days.
C. Mueller-Dieckmann, S. Panjikar, A. Schmidt, S. Mueller, J. Kuper, A. Geerlof, M. Wilmanns, R. Singh, P. Tucker, M. Weiss (2007)
On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.Acta crystallographica. Section D, Biological crystallography, 63 Pt 3
(2014)
Quarterly reviews of biophysics
E. Garman, C. Nave (2002)
Radiation damage to crystalline biological molecules: current view.Journal of synchrotron radiation, 9 Pt 6
D. Liebschner, Yusuke Yamada, N. Matsugaki, M. Senda, T. Senda (2016)
On the influence of crystal size and wavelength on native SAD phasing.Acta crystallographica. Section D, Structural biology, 72 Pt 6
Djinović Carugo (2005)
410J. Synchrotron Rad., 12
Acta Crystallographica Section D
(2006)
Nature ProtocolsNature Cell Biology, 8
F. Delaglio, S. Grzesiek, G. Vuister, G. Zhu, John Pfeifer, A. Bax (1995)
NMRPipe: A multidimensional spectral processing system based on UNIX pipesJournal of Biomolecular NMR, 6
A. Goulet, Gisle Vestergaard, C. Felisberto-Rodrigues, V. Campanacci, R. Garrett, C. Cambillau, M. Ortíz-Lombardía (2010)
Getting the best out of long-wavelength X-rays: de novo chlorine/sulfur SAD phasing of a structural protein from ATV.Acta crystallographica. Section D, Biological crystallography, 66 Pt 3
Selvi Bharathavikru, Tatiana Dudnakova (2016)
Methods Molecular Biology
Min-Kyu Kim, Sangmin Lee, Y. An, C. Jeong, Chang-Jun Ji, Jin-won Lee, S. Cha (2013)
In-house zinc SAD phasing at Cu Kα edgeMolecules and Cells, 36
M. Gadd, E. Bulatov, A. Ciulli (2015)
Serendipitous SAD Solution for DMSO-Soaked SOCS2-ElonginC-ElonginB Crystals Using Covalently Incorporated Dimethylarsenic: Insights into Substrate Receptor Conformational Flexibility in Cullin RING LigasesPLoS ONE, 10
S. Altschul, W. Gish, W. Miller, E. Myers, D. Lipman (1990)
Basic local alignment search tool.Journal of molecular biology, 215 3
(2005)
1437-1448. not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which was
O. Zeldin, M. Gerstel, E. Garman (2013)
RADDOSE-3D: time- and space-resolved modelling of dose in macromolecular crystallographyJournal of Applied Crystallography, 46
K. Carugo, J. Helliwell, H. Stuhrmann, M. Weiss (2005)
Softer and soft X-rays in macromolecular crystallography.Journal of synchrotron radiation, 12 Pt 4
Jin-Yi Zhu, Z. Fu, Lirong Chen, Hao Xu, J. Chrzas, J. Rose, Bi-Cheng Wang (2012)
Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal.Acta crystallographica. Section D, Biological crystallography, 68 Pt 9
(2016)
Biochemistry, 55, 1398–1407
Hendrickson (2014)
49Q. Rev. Biophys., 47
Dauter (1999)
93J. Mol. Biol., 289
Holton (2009)
133J. Synchrotron Rad., 16
Q. Shen, Jun Wang, S. Ealick (2003)
Anomalous difference signal in protein crystals.Acta crystallographica. Section A, Foundations of crystallography, 59 Pt 4
Brändén (1990)
687Nature (London), 343
H. Berman, Tammy Battistuz, T. Bhat, Wolfgang Bluhm, Philip Bourne, K. Burkhardt, Zukang Feng, G. Gilliland, L. Iype, Shri Jain, Phoebe Fagan, Jessica Marvin, David Padilla, V. Ravichandran, B. Schneider, N. Thanki, H. Weissig, J. Westbrook, C. Zardecki
Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank
W. Hendrickson (2014)
Anomalous diffraction in crystallographic phase evaluationQuarterly Reviews of Biophysics, 47
A. Wagner, M. Pieren, C. Schulze-Briese, K. Ballmer-Hofer, A. Prota (2006)
Structure determination of VEGF-E by sulfur SAD.Acta crystallographica. Section D, Biological crystallography, 62 Pt 11
K. Omari, O. Iourin, J. Kadlec, R. Fearn, D. Hall, K. Harlos, J. Grimes, D. Stuart (2014)
Pushing the limits of sulfur SAD phasing: de novo structure solution of the N-terminal domain of the ectodomain of HCV E1Acta Crystallographica Section D: Biological Crystallography, 70
Henderson (1990)
6Proc. R. Soc. B Biol. Sci., 241
D. Liebschner, Gerold Rosenbaum, M. Dauter, Z. Dauter (2015)
Radiation decay of thaumatin crystals at three X-ray energies.Acta crystallographica. Section D, Biological crystallography, 71 Pt 4
Xiang Liu, Heng Zhang, Xiao-jun Wang, Lan-fen Li, X. Su (2011)
Get Phases from Arsenic Anomalous Scattering: de novo SAD Phasing of Two Protein Structures Crystallized in Cacodylate BufferPLoS ONE, 6
Debreczeni (2003)
688Acta Cryst. D, 59
Carl-Ivar Bränd´en, T. Jones (1990)
Between objectivity and subjectivityNature, 343
K. Cowtan, K. Zhang (1999)
Density modification for macromolecular phase improvement.Progress in biophysics and molecular biology, 72 3
U. Ramagopal, M. Dauter, Z. Dauter
Electronic Reprint Biological Crystallography Phasing on Anomalous Signal of Sulfurs: What Is the Limit? Biological Crystallography Phasing on Anomalous Signal of Sulfurs: What Is the Limit?
A. Bangham (1965)
Progress in Biophysics and Molecular Biology, 14.Journal of the Royal Society of Medicine, 58
T. Weinert, V. Olieric, S. Waltersperger, E. Panepucci, Lirong Chen, Hua Zhang, Dayong Zhou, J. Rose, A. Ebihara, S. Kuramitsu, Dianfan Li, N. Howe, G. Schnapp, A. Pautsch, K. Bargsten, A. Prota, P. Surana, J. Kottur, D. Nair, Federica Basilico, V. Cecatiello, S. Pasqualato, A. Boland, O. Weichenrieder, Bi-Cheng Wang, M. Steinmetz, M. Caffrey, Meitian Wang (2014)
Fast native-SAD phasing for routine macromolecular structure determinationNature Methods, 12
Z. Dauter, D. Adamiak (2001)
Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy.Acta crystallographica. Section D, Biological crystallography, 57 Pt 7
I. Usón, B. Schmidt, R. Bülow, S. Grimme, K. Figura, M. Dauter, K. Rajashankar, Z. Dauter, G. Sheldrick (2003)
Locating the anomalous scatterer substructures in halide and sulfur phasing.Acta crystallographica. Section D, Biological crystallography, 59 Pt 1
G. Langer, Serge Cohen, V. Lamzin, A. Perrakis (2008)
Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7Nature Protocols, 3
B. Wang (1985)
Resolution of phase ambiguity in macromolecular crystallography.Methods in enzymology, 115
Uijin Kim, Dong-Sung Lee
Molecules and Cells
Goulet (2010)
304Acta Cryst. D, 66
P. Adams, P. Afonine, G. Bunkoczi, Vincent Chen, Ian Davis, N. Echols, J. Headd, Li-Wei Hung, Gary Kapral, R. Grosse-Kunstleve, A. Mccoy, N. Moriarty, R. Oeffner, R. Read, David Richardson, J. Richardson, Thomas Terwilliger, P. Zwart
Electronic Reprint Biological Crystallography Phenix : a Comprehensive Python-based System for Macromolecular Structure Solution
Shinji Watanabe, Yasuhiro Minami, Atsushi Nakamura, Naonori Ueda (1975)
An Asynchronous Hidden Markov Model for Audio-Visual Speech Recognition –
Dauter (2001)
990Acta Cryst. D, 57
Z. Dauter (2006)
Estimation of anomalous signal in diffraction data.Acta crystallographica. Section D, Biological crystallography, 62 Pt 8
Qun Liu, Tassadite Dahmane, Zhen Zhang, Zahra Assur, J. Brasch, L. Shapiro, F. Mancia, W. Hendrickson (2012)
Structures from Anomalous Diffraction of Native Biological MacromoleculesScience, 336
Bauman (2016)
51IUCrJ, 3
R. Henderson (1990)
Cryo-protection of protein crystals against radiation damage in electron and X-ray diffractionProceedings of the Royal Society of London. Series B: Biological Sciences, 241
(2006)
All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which was this version posted August 8
M. Cianci, M. Groves, D. Barford, T. Schneider (2016)
Data collection with a tailored X-ray beam size at 2.69 Å wavelength (4.6 keV): sulfur SAD phasing of Cdc23NtermActa Crystallographica. Section D, Structural Biology, 72
M. Winn, C. Ballard, K. Cowtan, E. Dodson, P. Emsley, P. Evans, R. Keegan, E. Krissinel, A. Leslie, A. Mccoy, S. McNicholas, G. Murshudov, N. Pannu, E. Potterton, H. Powell, R. Read, A. Vagin, K. Wilson (2011)
Overview of the CCP4 suite and current developmentsActa Crystallographica Section D: Biological Crystallography, 67
U. Ramagopal, M. Dauter, Z. Dauter (2003)
SAD manganese in two crystal forms of glucose isomerase.Acta crystallographica. Section D, Biological crystallography, 59 Pt 5
J. Doutch, M. Hough, S. Hasnain, R. Strange (2012)
Challenges of sulfur SAD phasing as a routine method in macromolecular crystallography.Journal of synchrotron radiation, 19 Pt 1
Akey (2014)
2719Acta Cryst. D, 70
D. Rodríguez, C. Grosse, S. Himmel, C. González, I. Ilarduya, S. Becker, G. Sheldrick, I. Usón (2009)
Crystallographic ab initio protein structure solution below atomic resolutionNature Methods, 6
V. Carapella, S. Niederer, M. Bishop, J. Schneider (1965)
Progress in Biophysics and Molecular BiologyMedical Journal of Australia, 1
P. Salgado, M. Walsh, Minni Laurila, D. Stuart, J. Grimes (2005)
Going soft and SAD with manganese.Acta crystallographica. Section D, Biological crystallography, 61 Pt 1
R. Ravelli, E. Garman (2006)
Radiation damage in macromolecular cryocrystallography.Current opinion in structural biology, 16 5
Zhi-jie Liu, E. Vysotski, Chun-Jung Chen, J. Rose, John Lee, Bi-Cheng Wang (2000)
Structure of the Ca2+‐regulated photoprotein obelin at 1.7 Å resolution determined directly from its sulfur substructureProtein Science, 9
(2002)
Journal of synchrotron radiation
T. Blundell, W. Hendrickson (2011)
What is 'current opinion' in structural biology?Current opinion in structural biology, 21 4
El Omari (2014)
2197Acta Cryst. D, 70
G. Sarma, P. Karplus (2006)
In-house sulfur SAD phasing: a case study of the effects of data quality and resolution cutoffs.Acta crystallographica. Section D, Biological crystallography, 62 Pt 7
Bunkóczi (2015)
127Nature Methods, 12
Garman (2002)
327J. Synchrotron Rad., 9
W. Minor, M. Cymborowski, Z. Otwinowski, M. Chruszcz (2006)
HKL-3000: the integration of data reduction and structure solution--from diffraction images to an initial model in minutes.Acta crystallographica. Section D, Biological crystallography, 62 Pt 8
Victor Hernandez, M. Bortolozzi, V. Pertegato, M. Beltramello, M. Giarin, M. Zaccolo, S. Pantano, F. Mammano (2007)
Nature Methods
Gadd (2015)
e0131218PLoS One, 10
(1990)
Proceedings: Biological Sciences
Hendrickson (1981)
107Nature (London), 290
A. Thorn, G. Sheldrick (2011)
ANODE: anomalous and heavy-atom density calculationJournal of Applied Crystallography, 44
P. Zwart (2005)
Anomalous signal indicators in protein crystallography.Acta crystallographica. Section D, Biological crystallography, 61 Pt 11
M. Gorgel, A. Boggild, J. Ulstrup, M. Weiss, U. Müller, P. Nissen, T. Boesen (2015)
Against the odds? De novo structure determination of a pilin with two cysteine residues by sulfur SAD.Acta crystallographica. Section D, Biological crystallography, 71 Pt 5
T. Pape, T. Schneider (2004)
HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programsJournal of Applied Crystallography, 37
G. Bunkoczi, A. Mccoy, N. Echols, R. Grosse-Kunstleve, P. Adams, J. Holton, R. Read, T. Terwilliger (2014)
Macromolecular X-ray structure determination using weak single-wavelength anomalous dataNature methods, 12
J. Holton (2009)
A beginner’s guide to radiation damageJournal of Synchrotron Radiation, 16
A. Deshpande, K. Wagenpfeil, T. Pochapsky, G. Petsko, D. Ringe (2016)
Metal-Dependent Function of a Mammalian Acireductone Dioxygenase.Biochemistry, 55 9
R. Owen, E. Rudiño-Piñera, E. Garman (2006)
Experimental determination of the radiation dose limit for cryocooled protein crystals.Proceedings of the National Academy of Sciences of the United States of America, 103 13
Z. Dauter, M. Dauter (1999)
Anomalous signal of solvent bromides used for phasing of lysozyme.Journal of molecular biology, 289 1
Hendrickson (1990)
1665EMBO J., 9
Z. Otwinowski, W. Minor (1997)
[20] Processing of X-ray diffraction data collected in oscillation mode.Methods in enzymology, 276
K. Lakomek, A. Dickmanns, U. Mueller, K. Kollmann, F. Deuschl, Annette Berndt, T. Lübke, R. Ficner (2009)
De novo sulfur SAD phasing of the lysosomal 66.3 kDa protein from mouse.Acta crystallographica. Section D, Biological crystallography, 65 Pt 3
(1959)
Journal of Molecular BiologyNature, 183
J. Debreczeni, G. Bunkoczi, Q. Ma, Heiko Blaser, G. Sheldrick (2003)
In-house measurement of the sulfur anomalous signal and its use for phasing.Acta crystallographica. Section D, Biological crystallography, 59 Pt 4
W. Shi, H. Robinson, M. Sullivan, D. Abel, J. Toomey, L. Berman, D. Lynch, G. Rosenbaum, G. Rakowsky, L. Rock, B. Nolan, G. Shea-Mccarthy, D. Schneider, Erik Johnson, R. Sweet, M. Chance (2006)
Beamline X29: a novel undulator source for X-ray crystallography.Journal of synchrotron radiation, 13 Pt 5
W. Delano (2002)
The PyMOL Molecular Graphics System
Dauter (2006)
867Acta Cryst. D, 62
Cuesta-Seijo (2006)
417Acta Cryst. D, 62
S. Banumathi, P. Zwart, U. Ramagopal, M. Dauter, Z. Dauter
Biological Crystallography Structural Effects of Radiation Damage and Its Potential for Phasing
Gorgel (2015)
1095Acta Cryst. D, 71
M. Dauter, Z. Dauter (2007)
Phase determination using halide ions.Methods in molecular biology, 364
J. Bauman, J. Harrison, E. Arnold (2016)
Rapid experimental SAD phasing and hot-spot identification with halogenated fragmentsIUCrJ, 3
G. Murshudov, P. Skubák, A. Lebedev, N. Pannu, R. Steiner, R. Nicholls, M. Winn, F. Long, A. Vagin (2011)
REFMAC5 for the refinement of macromolecular crystal structuresActa Crystallographica Section D: Biological Crystallography, 67
Jiawei Wang, M. Dauter, Z. Dauter
Electronic Reprint Biological Crystallography What Can Be Done with a Good Crystal and an Accurate Beamline? Biological Crystallography What Can Be Done with a Good Crystal and an Accurate Beamline?
Berman (2000)
235Nucleic Acids Res., 28
玉一 芦田 (1993)
Acta Crystallographica Section D (Biological Crystallography) の発刊に際して, 35
E. Garman (2010)
Radiation damage in macromolecular crystallography: what is it and why should we care?Acta Crystallographica Section D: Biological Crystallography, 66
Altschul (1990)
403J. Mol. Biol., 215
(2000)
Nucleic acids research 28
Banumathi (2004)
1085Acta Cryst. D, 60
Doutch (2012)
19J. Synchrotron Rad., 19
Z. Dauter, M. Dauter, E. Fortelle, G. Bricogne, G. Sheldrick (1999)
Can anomalous signal of sulfur become a tool for solving protein crystal structures?Journal of molecular biology, 289 1
Qun Liu, Youzhong Guo, Yanqi Chang, Z. Cai, Zahra Assur, F. Mancia, M. Greene, W. Hendrickson (2014)
Multi-crystal native SAD analysis at 6 keV.Acta crystallographica. Section D, Biological crystallography, 70 Pt 10
(1990)
Proceedings of the National Academy of Sciences of the United States of America. Annual subject and author indexes.Proceedings of the National Academy of Sciences of the United States of America, 87 Suppl
Jurgis Sūdžius, Lina Baranauskienė, D. Golovenko, J. Matulienė, V. Michailovienė, Jolanta Torresan, Jelena Jachno, R. Sukackaitė, E. Manakova, S. Gražulis, S. Tumkevičius, D. Matulis (2010)
4-[N-(substituted 4-pyrimidinyl)amino]benzenesulfonamides as inhibitors of carbonic anhydrase isozymes I, II, VII, and XIII.Bioorganic & medicinal chemistry, 18 21
E. McClelland, U. Ramagopal, Johanna Rivera, James Cox, A. Nakouzi, M. Prabu, S. Almo, A. Casadevall (2016)
A Small Protein Associated with Fungal Energy Metabolism Affects the Virulence of Cryptococcus neoformans in MammalsPLoS Pathogens, 12
(2011)
PloS one 6
Michael Koch, J. Diez, A. Wagner, G. Fritz (2010)
Crystallization and calcium/sulfur SAD phasing of the human EF-hand protein S100A2.Acta crystallographica. Section F, Structural biology and crystallization communications, 66 Pt 9
T. Creighton (1968)
Methods in EnzymologyThe Yale Journal of Biology and Medicine, 40
Soichi Wakatsuki (1948)
Acta CrystallographicaNature, 161
J. Cuesta-Seijo, M. Weiss, G. Sheldrick (2006)
Serendipitous SAD phasing of an echinomycin-(ACGTACGT)2 bisintercalation complex.Acta crystallographica. Section D, Biological crystallography, 62 Pt 4
W. Hendrickson, J. Horton, D. LeMaster (1990)
Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three‐dimensional structure.The EMBO Journal, 9
D. Rodríguez, M. Sammito, K. Meindl, Iñaki Ilarduya, Marianus Potratz, G. Sheldrick, I. Usón (2012)
Practical structure solution with ARCIMBOLDOActa Crystallographica Section D: Biological Crystallography, 68
M. Weiss, T. Sicker, R. Hilgenfeld (2001)
Soft X-rays, high redundancy, and proper scaling: a new procedure for automated protein structure determination via SAS.Structure, 9 9
T. Terwilliger, G. Bunkoczi, L. Hung, P. Zwart, Janet Smith, D. Akey, P. Adams (2016)
Can I solve my structure by SAD phasing? Anomalous signal in SAD phasingActa Crystallographica. Section D, Structural Biology, 72
(1991)
Proc. Of ccp4 study weekend on isomorphous replacement and anomalous scattering
W. Hendrickson, M. Teeter (1981)
Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulphurNature, 290
J. Rose, Bi-Cheng Wang, M. Weiss (2015)
Native SAD is maturingIUCrJ, 2
G. Sheldrick (2010)
Experimental phasing with SHELXC/D/E: combining chain tracing with density modificationActa Crystallographica Section D: Biological Crystallography, 66
Cowtan (1999)
245Prog. Biophys. Mol. Biol., 72
Dauter (1999)
83J. Mol. Biol., 289
E. Micossi, W. Hunter, G. Leonard (2002)
De novo phasing of two crystal forms of tryparedoxin II using the anomalous scattering from S atoms: a combination of small signal and medium resolution reveals this to be a general tool for solving protein crystal structures.Acta crystallographica. Section D, Biological crystallography, 58 Pt 1
D. Akey, W. Brown, Jamie Konwerski, C. Ogata, Janet Smith (2014)
Use of massively multiple merged data for low-resolution S-SAD phasing and refinement of flavivirus NS1.Acta crystallographica. Section D, Biological crystallography, 70 Pt 10
Adams (2010)
213Acta Cryst. D, 66
Cianci (2016)
403Acta Cryst. D, 72
Deshpande (2016)
1398Biochemistry, 55
Garman (2010)
339Acta Cryst. D, 66
Dauter (2007)
149Methods Mol. Biol., 364
Single‐wavelength anomalous dispersion (SAD) utilizing anomalous signal from native S atoms, or other atoms with Z ≤ 20, generally requires highly redundant data collected using relatively long‐wavelength X‐rays. Here, the results from two proteins are presented where the anomalous signal from serendipitously acquired surface‐bound Ca atoms with an anomalous data multiplicity of around 10 was utilized to drive de novo structure determination. In both cases, the Ca atoms were acquired from the crystallization solution, and the data‐collection strategy was not optimized to exploit the anomalous signal from these scatterers. The X‐ray data were collected at 0.98 Å wavelength in one case and at 1.74 Å in the other (the wavelength was optimized for sulfur, but the anomalous signal from calcium was exploited for structure solution). Similarly, using a test case, it is shown that data collected at ∼1.0 Å wavelength, where the f′′ value for sulfur is 0.28 e, are sufficient for structure determination using intrinsic S atoms from a strongly diffracting crystal. Interestingly, it was also observed that SHELXD was capable of generating a substructure solution from high‐exposure data with a completeness of 70% for low‐resolution reflections extending to 3.5 Å resolution with relatively low anomalous multiplicity. Considering the fact that many crystallization conditions contain anomalous scatterers such as Cl, Ca, Mn etc., checking for the presence of fortuitous anomalous signal in data from well diffracting crystals could prove useful in either determining the structure de novo or in accurately assigning surface‐bound atoms.
Acta Crystallographica Section F – Wiley
Published: Jan 1, 2017
Keywords: ;
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.