Two-wavelength MAD phasing: in search of the optimal choice of wavelengths

1999 ◽  
Vol 55 (8) ◽  
pp. 1449-1458 ◽  
Author(s):  
A. González ◽  
J.-D. Pédelacq ◽  
M. Solà ◽  
F. X. Gomis-Rüth ◽  
M. Coll ◽  
...  
Keyword(s):  
Data Collection ◽  
Crystal Structures ◽  
Optimal Choice ◽  
Protein Crystal ◽  
Anomalous Scattering ◽  
Mad Phasing ◽  
Data Collection Strategy ◽  
Different Types ◽  
Scattering Factor

The multiwavelength anomalous dispersion (MAD) method is increasingly being used to determine protein crystal structures. In theory, data collection at two wavelengths is sufficient for the determination of MAD phases, but three or even more wavelengths are used most often. In this paper, the results of the phasing procedure using only two wavelengths for proteins containing different types of anomalous scatterers are analyzed. In these cases, it is shown that this approach leads to interpretable maps, similar in quality to those obtained with data collected at three wavelengths, provided that the wavelengths are chosen so as to give a large contrast in the real part of the anomalous scattering factor f. The consequences for a rational MAD data-collection strategy are discussed.

scholarly journals Approaches to automated protein crystal harvesting

2014 ◽  
Vol 70 (2) ◽  
pp. 133-155 ◽  
Author(s):  
Marc C. Deller ◽  
Bernhard Rupp
Keyword(s):  
Data Collection ◽  
Single Step ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Optical Traps ◽  
Fourth Generation ◽  
Flash Cooling ◽  
Harvesting Systems ◽  
Harvesting Process

The harvesting of protein crystals is almost always a necessary step in the determination of a protein structure using X-ray crystallographic techniques. However, protein crystals are usually fragile and susceptible to damage during the harvesting process. For this reason, protein crystal harvesting is the single step that remains entirely dependent on skilled human intervention. Automation has been implemented in the majority of other stages of the structure-determination pipeline, including cloning, expression, purification, crystallization and data collection. The gap in automation between crystallization and data collection results in a bottleneck in throughput and presents unfortunate opportunities for crystal damage. Several automated protein crystal harvesting systems have been developed, including systems utilizing microcapillaries, microtools, microgrippers, acoustic droplet ejection and optical traps. However, these systems have yet to be commonly deployed in the majority of crystallography laboratories owing to a variety of technical and cost-related issues. Automation of protein crystal harvesting remains essential for harnessing the full benefits of fourth-generation synchrotrons, free-electron lasers and microfocus beamlines. Furthermore, automation of protein crystal harvesting offers several benefits when compared with traditional manual approaches, including the ability to harvest microcrystals, improved flash-cooling procedures and increased throughput.

Determination of Anomalous Scattering Factor by Using Transmitted Rocking Curves near the Absorption Edge

1997 ◽  
Vol 36 (Part 1, No. 10) ◽  
pp. 6424-6425 ◽  
Author(s):  
Shengming Zhou ◽  
Masami Yoshizawa ◽  
Tomoe Fukamachi ◽  
Riichiro Negishi ◽  
Takaaki Kawamura ◽  
...  
Keyword(s):  
Absorption Edge ◽  
Anomalous Scattering ◽  
Scattering Factor

Removing bias from solvent atoms in electron density maps

2008 ◽  
Vol 41 (4) ◽  
pp. 761-767 ◽  
Author(s):  
Eric N. Brown
Keyword(s):  
Crystal Structures ◽  
Electron Density ◽  
Protein Crystal ◽  
Water Molecules ◽  
Data Set ◽  
Atomic Structures ◽  
Research Article ◽  
Density Maps ◽  
Atom Position

Atomic structures of proteins determinedviaprotein crystallography contain numerous solvent atoms. The experimental data for the determination of a water molecule's O-atom position is often a small contained blob of unidentified electron density. Unfortunately, the nature of crystallographic refinement lets poorly placed solvent atoms bias the future refined positions of all atoms in the crystal structure. This research article presents the technique of omit-maps applied to remove the bias introduced by poorly determined solvent atoms, enabling the identification of incorrectly placed water molecules in partially refined crystal structures. A total of 160 protein crystal structures with 45 912 distinct water molecules were processed using this technique. Most of the water molecules in the deposited structures were well justified. However, a few of the solvent atoms in this test data set changed appreciably in position, displacement parameter or electron density when fitted to the solvent omit-map, raising questions about how much experimental support exists for these solvent atoms.

scholarly journals Long-wavelength native-SAD phasing: opportunities and challenges

IUCrJ ◽  
2019 ◽  
Vol 6 (3) ◽  
pp. 373-386 ◽  
Author(s):  
Shibom Basu ◽  
Vincent Olieric ◽  
Filip Leonarski ◽  
Naohiro Matsugaki ◽  
Yoshiaki Kawano ◽  
...  
Keyword(s):  
Anomalous Scattering ◽  
X Rays ◽  
X Ray ◽  
Long Wavelength ◽  
Experimental Phasing ◽  
Sad Phasing ◽  
Anomalous Signal ◽  
Scattering Factor ◽  
X Ray Absorption

Native single-wavelength anomalous dispersion (SAD) is an attractive experimental phasing technique as it exploits weak anomalous signals from intrinsic light scatterers (Z < 20). The anomalous signal of sulfur in particular, is enhanced at long wavelengths, however the absorption of diffracted X-rays owing to the crystal, the sample support and air affects the recorded intensities. Thereby, the optimal measurable anomalous signals primarily depend on the counterplay of the absorption and the anomalous scattering factor at a given X-ray wavelength. Here, the benefit of using a wavelength of 2.7 over 1.9 Å is demonstrated for native-SAD phasing on a 266 kDa multiprotein-ligand tubulin complex (T2R-TTL) and is applied in the structure determination of an 86 kDa helicase Sen1 protein at beamline BL-1A of the KEK Photon Factory, Japan. Furthermore, X-ray absorption at long wavelengths was controlled by shaping a lysozyme crystal into spheres of defined thicknesses using a deep-UV laser, and a systematic comparison between wavelengths of 2.7 and 3.3 Å is reported for native SAD. The potential of laser-shaping technology and other challenges for an optimized native-SAD experiment at wavelengths >3 Å are discussed.

Determination of the Anomalous Scattering Factors in the Soft-X-ray Range using Diffraction from a Multilayer

1998 ◽  
Vol 31 (5) ◽  
pp. 700-707 ◽  
Author(s):  
L. Sève ◽  
J. M. Tonnerre ◽  
D. Raoux
Keyword(s):  
Fluorescence Yield ◽  
Bragg Diffraction ◽  
Anomalous Scattering ◽  
Total Electron Yield ◽  
Total Electron ◽  
X Ray ◽  
Scattering Factor ◽  
X Ray Absorption ◽  
Kronig Relation

Bragg diffraction from an Ag/Ni multilayer was used to determine independently both the real and imaginary parts of the anomalous scattering factor (ASF) around the NiLIIIandLIIedges in the soft-X-ray range. Huge resonant variations were observed with f'' reaching 55\,r_o and f' decreasing to −63 r_o at the NiLIIIedge. The independent measurements of f' and f'' are tested for coherency using the Kramers–Kronig relation. The f'' values are also compared with those derived from X-ray absorption methods such as total electron yield and fluorescence yield measurements.

Determination of the anomalous scattering factors for Cu, Ni and Ti using the dispersion relation

1984 ◽  
Vol 17 (5) ◽  
pp. 344-351 ◽  
Author(s):  
J. J. Hoyt ◽  
D. de Fontaine ◽  
W. K. Warburton
Keyword(s):  
Dispersion Relation ◽  
Optical Theorem ◽  
Anomalous Scattering ◽  
X Ray ◽  
Atomic Scattering ◽  
Experimental Errors ◽  
Scattering Factor ◽  
Radiation Laboratory ◽  
X Ray Absorption

X-ray absorption spectra about the K edges of Ni, Cu and Ti have been measured at the Stanford Synchrotron Radiation Laboratory. The imaginary part of the atomic scattering factor f′′ was determined using the optical theorem and the real part f′ computed by the Kramers–Kronig dispersion relation. Methods for evaluating this integral as well as the effects on f′ of various experimental errors are investigated. The f′ results for Cu and Ni are compared to data from interferometry experiments.

scholarly journals Unsupervised determination of protein crystal structures

2019 ◽  
Vol 116 (22) ◽  
pp. 10813-10818 ◽  
Author(s):  
Ivan S. Ufimtsev ◽  
Michael Levitt
Keyword(s):  
Crystal Structures ◽  
Protein Crystal ◽  
Search Model ◽  
Molecular Replacement ◽  
Initial Model ◽  
Large Pool

We present a method for automatic solution of protein crystal structures. The method proceeds with a single initial model obtained, for instance, by molecular replacement (MR). If a good-quality search model is not available, as often is the case with MR of distant homologs, our method first can automatically screen a large pool of poorly placed models and single out promising candidates for further processing if there are any. We demonstrate its utility by solving a set of synthetic cases in the 2.9- to 3.45-Å resolution.

scholarly journals DETERMINATION OF ANOMALOUS SCATTERING FACTOR FOR Ga BY USING ROCKING CURVES OF TRANSMITTED BEAM IN GaAs

1996 ◽  
Vol 45 (11) ◽  
pp. 1846
Author(s):  
ZHOU SHENG-MING ◽  
ZHAO ZONG-YAN ◽  
HAN JIA-HUA ◽  
HU YU-GEN ◽  
TOMOE FUKAMACHI ◽  
...  
Keyword(s):  
Anomalous Scattering ◽  
Transmitted Beam ◽  
Scattering Factor
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