scholarly journals Native SAD Structure Solution from Merohedrally Twinned Data

2014 ◽  
Vol 70 (a1) ◽  
pp. C614-C614
Author(s):  
Tobias Weinert ◽  
Sandro Waltersperger ◽  
Vincent Olieric ◽  
Federica Basilico ◽  
Valentina Cecatiello ◽  
...  
Keyword(s):  
Light Source ◽  
Model Building ◽  
Experimental Setup ◽  
Difficult Case ◽  
Space Group ◽  
Human Centromere ◽  
Centromere Protein ◽  
Structure Solution ◽  
Swiss Light Source ◽  
Automatic Model Building

Up until now, comparatively few structures were solved by native SAD. Recent advances in multi crystal averaging [1] have shown that native SAD can be applied to an increasing number of cases. Though theoretically possible [2], successful structure solutions from twinned data have not been reported yet. Here, we report the structure solution of the human Centromere protein M from a merohedrally twinned crystal with a twinning fraction of 0.45 in the space group P3. The data were collected at the bending magnet beamline X06DA at the Swiss Light Source, which is equipped with the in-house developed multi-axis goniometer PRIGo and the PILATUS 2M detector. A highly redundant 2.2 Å dataset was collected in a number of different crystal orientations. A substructure solution could only be obtained after 50000 SHELXD [3] tries. Automatic model building after phasing and density modification resulted in a model with the majority of residues built correctly. We will present this particularly difficult case together with other more routine cases, all solved with the same experimental setup and at the beamline X06DA.

scholarly journals Making routine native SAD a reality: lessons from beamline X06DA at the Swiss Light Source

2019 ◽  
Vol 75 (3) ◽  
pp. 262-271 ◽  
Author(s):  
Shibom Basu ◽  
Aaron Finke ◽  
Laura Vera ◽  
Meitian Wang ◽  
Vincent Olieric
Keyword(s):  
Data Collection ◽  
Light Source ◽  
Low Dose ◽  
Model Building ◽  
De Novo ◽  
Anomalous Scattering ◽  
Orientation Data ◽  
Swiss Light Source ◽  
Experimental Phasing ◽  
Sad Phasing

Native single-wavelength anomalous dispersion (SAD) is the most attractive de novo phasing method in macromolecular crystallography, as it directly utilizes intrinsic anomalous scattering from native crystals. However, the success of such an experiment depends on accurate measurements of the reflection intensities and therefore on careful data-collection protocols. Here, the low-dose, multiple-orientation data-collection protocol for native SAD phasing developed at beamline X06DA (PXIII) at the Swiss Light Source is reviewed, and its usage over the last four years on conventional crystals (>50 µm) is reported. Being experimentally very simple and fast, this method has gained popularity and has delivered 45 de novo structures to date (13 of which have been published). Native SAD is currently the primary choice for experimental phasing among X06DA users. The method can address challenging cases: here, native SAD phasing performed on a streptavidin–biotin crystal with P21 symmetry and a low Bijvoet ratio of 0.6% is highlighted. The use of intrinsic anomalous signals as sequence markers for model building and the assignment of ions is also briefly described.

scholarly journals Lysozyme contamination facilitates crystallization of a heterotrimeric cortactin–Arg–lysozyme complex

2012 ◽  
Vol 68 (2) ◽  
pp. 154-158 ◽  
Author(s):  
Weizhi Liu ◽  
Stacey M. MacGrath ◽  
Anthony J. Koleske ◽  
Titus J. Boggon
Keyword(s):  
Crystal Structure ◽  
Model Building ◽  
Protein A ◽  
Molecular Replacement ◽  
Caveat Emptor ◽  
Nonreceptor Tyrosine Kinase ◽  
Structure Solution ◽  
Automatic Model Building ◽  
Cocrystal Structure

Crystallization of contaminating proteins is a frequently encountered problem for macromolecular crystallographers. In this study, an attempt was made to obtain a binary cocrystal structure of the SH3 domain of cortactin and a 17-residue peptide from the Arg nonreceptor tyrosine kinase encompassing a PxxPxxPxxP (PxxP1) motif. However, cocrystals could only be obtained in the presence of trace amounts of a contaminating protein. A structure solution obtained by molecular replacement followed byARP/wARPautomatic model building allowed a `sequence-by-crystallography' approach to discover that the contaminating protein was lysozyme. This 1.65 Å resolution crystal structure determination of a 1:1:1 heterotrimeric complex of Arg, cortactin and lysozyme thus provides an unusual `caveat emptor' warning of the dangers that underpurified proteins harbor for macromolecular crystallographers.

scholarly journals Kinetics of 1- and 2-methylallyl + O2 reaction, investigated by photoionisation using synchrotron radiation

2021 ◽  
Author(s):  
Domenik Schleier ◽  
Engelbert Reusch ◽  
Marius Gerlach ◽  
Tobias Preitschopf ◽  
Deb Pratim Mukhopadhyay ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Reaction Kinetics ◽  
Molecular Oxygen ◽  
Light Source ◽  
Storage Ring ◽  
Vacuum Ultraviolet ◽  
Flow Tube ◽  
Tube Reactor ◽  
Swiss Light Source ◽  
Kinetics Of

The reaction kinetics of the isomers of the methylallyl radical with molecular oxygen has been studied in a flow tube reactor at the vacuum ultraviolet (VUV) beamline of the Swiss Light Source storage ring.

Towards the automatic crystal structure solution of nucleic acids: automated model building using the new CAB program

2021 ◽  
Vol 77 (12) ◽  
Author(s):  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo
Keyword(s):  
Nucleic Acids ◽  
Prior Information ◽  
Model Building ◽  
Phase Error ◽  
Heavy Atoms ◽  
Density Maps ◽  
Structure Solution ◽  
Nucleic Acid Structures ◽  
Automated Model Building ◽  
Model Chain

CAB, a recently described automated model-building (AMB) program, has been modified to work effectively with nucleic acids. To this end, several new algorithms have been introduced and the libraries have been updated. To reduce the input average phase error, ligand heavy atoms are now located before starting the CAB interpretation of the electron-density maps. Furthermore, alternative approaches are used depending on whether the ligands belong to the target or to the model chain used in the molecular-replacement step. Robust criteria are then applied to decide whether the AMB model is acceptable or whether it must be modified to fit prior information on the target structure. In the latter case, the model chains are rearranged to fit prior information on the target chains. Here, the performance of the new AMB program CAB applied to various nucleic acid structures is discussed. Other well documented programs such as Nautilus, ARP/wARP and phenix.autobuild were also applied and the experimental results are described.

scholarly journals High-resolution 3D scanning X-ray microscopes at the Swiss Light Source

2018 ◽  
Vol 24 (S2) ◽  
pp. 172-175 ◽  
Author(s):  
Mirko Holler ◽  
Jorg Raabe ◽  
Ana Diaz ◽  
Manuel Guizar-Sicairos ◽  
Esther H. R. Tsai ◽  
...  
Keyword(s):  
High Resolution ◽  
Light Source ◽  
3D Scanning ◽  
X Ray ◽  
Swiss Light Source

X-ray tomographic microscopy at the Swiss Light Source

2002 ◽  
Author(s):  
Marco Stampanoni ◽  
Peter Wyss ◽  
Rafael Abela ◽  
Gunther L. Borchert ◽  
Detlef Vermeulen ◽  
...  
Keyword(s):  
Light Source ◽  
X Ray ◽  
Swiss Light Source

scholarly journals Determination of X-ray flux using silicon pin diodes

2009 ◽  
Vol 16 (2) ◽  
pp. 143-151 ◽  
Author(s):  
Robin L. Owen ◽  
James M. Holton ◽  
Clemens Schulze-Briese ◽  
Elspeth F. Garman
Keyword(s):  
Light Source ◽  
Energy Deposition ◽  
Photon Flux ◽  
Macromolecular Crystallography ◽  
Pin Diodes ◽  
Web Based ◽  
X Ray ◽  
Swiss Light Source ◽  
Flux Incident

Accurate measurement of photon flux from an X-ray source, a parameter required to calculate the dose absorbed by the sample, is not yet routinely available at macromolecular crystallography beamlines. The development of a model for determining the photon flux incident on pin diodes is described here, and has been tested on the macromolecular crystallography beamlines at both the Swiss Light Source, Villigen, Switzerland, and the Advanced Light Source, Berkeley, USA, at energies between 4 and 18 keV. These experiments have shown that a simple model based on energy deposition in silicon is sufficient for determining the flux incident on high-quality silicon pin diodes. The derivation and validation of this model is presented, and a web-based tool for the use of the macromolecular crystallography and wider synchrotron community is introduced.

scholarly journals Expression, purification, crystallization and preliminary crystallographic analysis of the phosphoglycerate kinase fromAcinetobacter baumannii

2012 ◽  
Vol 68 (7) ◽  
pp. 790-792
Author(s):  
Kayla Baretta ◽  
Craig Garen ◽  
Jiang Yin ◽  
Michael N. G. James
Keyword(s):  
Synchrotron Radiation ◽  
Acinetobacter Baumannii ◽  
Light Source ◽  
Phosphoglycerate Kinase ◽  
Multidrug Resistant ◽  
Crystallographic Analysis ◽  
Lithium Sulfate ◽  
Space Group ◽  
Antibiotic Development ◽  
Potential Target

Acinetobacter baumanniiis a common multidrug-resistant clinical pathogen that is often found in hospitals. TheA. baumanniiphosphoglycerate kinase (AbPGK) is involved in the key energy-producing pathway of glycolysis and presents a potential target for antibiotic development.AbPGK has been expressed and purified; it was crystallized using lithium sulfate as the precipitant. TheAbPGK crystals belonged to space groupP2221. They diffracted to a resolution of 2.5 Å using synchrotron radiation at the Canadian Light Source.

Die Kristallstruktur des Lithium-Benzamidinats {Li3[C6H5 - C(NSiMe3)2]3 · NC - C6H5} / The Crystal Structure of the Lithium Phenylamidinate {Li3[C6H5 - C(NSiMe3)2]3 · NC - C6H5}

1994 ◽  
Vol 49 (10) ◽  
pp. 1444-1447 ◽  
Author(s):  
Helmut Goesmann ◽  
Dieter Fenske
Keyword(s):  
Crystal Structure ◽  
Nitrogen Atom ◽  
Single Crystals ◽  
Title Compound ◽  
The Other ◽  
Space Group ◽  
Structure Solution

AbstractSingle crystals of the title compound have been prepared by the reaction of benzonitrile with LiN-(SiMe3)2 in hexane and subsequent evaporation of the solvent. Space group P21/n, Z = 4, structure solution with 7945 observed unique reflections. R = 0.052. Lattice dimensions at -70 °C: a = 1485.2(9); b = 2486.9(11); c = 1568.9(8) pm; β = 91.06(4)°. The compound forms a trimeric ion ensemble in which two of the lithium cations are coordinated by three nitrogen atoms of two phenylamidinate an ions, the other one by four nitrogen atoms of two chelating phenylaminidate anions and in addition by the nitrogen atom of a benzonitrile molecule.

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