Anomalous dispersion analyses of the Ni-atom site in an aluminophosphate test crystal including the use of tuned synchrotron radiation

1996 ◽  
Vol 52 (3) ◽  
pp. 479-486 ◽  
Author(s):  
M. Helliwell ◽  
J. R. Helliwell ◽  
A. Cassetta ◽  
J. C. Hanson ◽  
T. Ericsson ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Data Sets ◽  
Acta Cryst ◽  
Data Set ◽  
Difference Map ◽  
Chemical Crystallography ◽  
Synchrotron Light ◽  
The Difference ◽  
Difference Fourier ◽  
Atom Position

Data were collected close to the Ni K edge, using synchrotron radiation at the National Synchrotron Light Source, and using a Mo Kα rotating anode, from a crystal of a nickel-containing aluminophosphate, NiAl3P4O18C4H21N4 (NiAPO). These data sets, along with an existing Cu Kα rotating anode data set, allowed the calculation of several f′ difference-Fourier maps exploiting the difference in f′ for Ni between the various wavelengths. These differences are expected to be 7.8, 4.5 and 3.3 e for Mo Kα data to SR (synchrotron radiation), Cu Kα to SR and Mo Kα to Cu Kα, respectively. The phases were calculated either excluding the Ni atom or with Al at the Ni-atom site. The f′ difference-Fourier maps revealed peaks at the Ni-atom site, whose height and distance from the refined Ni-atom position depended on the f' difference and the phase set used. The largest peak was located at a distance of only 0.025 Å from the refined Ni-atom site and was obtained from the f′ difference map calculated with the coefficients |F Mo Kα − F SR| , using phases calculated with Al at the Ni-atom site. In all cases, it was found that these phases gave optimal results without introducing bias into the maps. The results confirm and expand upon earlier results [Helliwell, Gallois, Kariuki, Kaučič & Helliwell (1993), Acta Cryst. B49, 420–428]. The techniques described are generally applicable to other systems containing anomalous scatterers in chemical crystallography.

Difference Fourier Analysis of Glucose Embedded and Frozen Hydrated Purple Membrane

1982 ◽  
Vol 40 ◽  
pp. 74-75
Author(s):  
Jules S. Jaffe ◽  
Robert M. Glaeser
Keyword(s):  
Purple Membrane ◽  
Data Set ◽  
High Resolution Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Fourier Techniques ◽  
Versus Protein ◽  
The Difference ◽  
Difference Fourier ◽  
Ideal Method

Although difference Fourier techniques are standard in X-ray crystallography it has only been very recently that electron crystallographers have been able to take advantage of this method. We have combined a high resolution data set for frozen glucose embedded Purple Membrane (PM) with a data set collected from PM prepared in the frozen hydrated state in order to visualize any differences in structure due to the different methods of preparation. The increased contrast between protein-ice versus protein-glucose may prove to be an advantage of the frozen hydrated technique for visualizing those parts of bacteriorhodopsin that are embedded in glucose. In addition, surface groups of the protein may be disordered in glucose and ordered in the frozen state. The sensitivity of the difference Fourier technique to small changes in structure provides an ideal method for testing this hypothesis.

Determination of the site of incorporation of cobalt in CoZnPO-CZP by multiple-wavelength anomalous-dispersion crystallography

1999 ◽  
Vol 55 (3) ◽  
pp. 327-332 ◽  
Author(s):  
M. Helliwell ◽  
J. R. Helliwell ◽  
V. Kaucic ◽  
N. Zabukovec Logar ◽  
L. Barba ◽  
...  
Keyword(s):  
Metal Atom ◽  
Peak Height ◽  
Data Sets ◽  
White Line ◽  
Data Set ◽  
Small Peak ◽  
Multiple Wavelength ◽  
Subsequent Calculation ◽  
Difference Fourier ◽  
Two Peaks

Data were collected from a crystal of CoZnPO-CZP {sodium cobalt–zinc phosphate hydrate, Na6[Co0.2Zn0.8PO4]6.6H2O} using synchrotron radiation at ELETTRA at the inflection point and `white line' for both the cobalt and zinc K edges, and at 1.45 Å, a wavelength remote from the K edges of both metals. The data were processed using the programs DENZO and SCALEPACK. The CCP4 program suite was used for the scaling of data sets and the subsequent calculation of dispersive difference Fourier maps. Optimal scaling was achieved by using a subset of reflections with little or no contribution from the metal atoms (i.e. which were essentially wavelength independent in their intensities) and using weights based on the σ's to obtain an overall scale factor in each case. Phases were calculated with SHELXL97 based on the refined structure using a much higher resolution and complete Cu Kα data set. An occupancy of 100% by zinc at the two metal-atom sites was assumed. The dispersive difference Fourier map calculated for zinc gave two peaks above the background of similar heights at the expected metal-atom sites. The peak height at the Zn1 site was a little higher than at the Zn2 site. The dispersive difference Fourier map calculated for cobalt gave just one peak above the background, at the Zn1 site, and only a small peak at the Zn2 site, thus indicating that incorporation of cobalt takes place mainly at one site. Refinement of the zinc occupancies using MLPHARE reinforces this conclusion. The chemical environment of each site is discussed.

A Ccomparison of sedigraph and pipette methods for soil particle-size analysis

Soil Research ◽  
1993 ◽  
Vol 31 (4) ◽  
pp. 407 ◽  
Author(s):  
GD Buchan ◽  
KS Grewal ◽  
JJ Claydon ◽  
RJ Mcpherson
Keyword(s):  
Particle Size ◽  
New Zealand ◽  
Particle Size Analysis ◽  
Size Analysis ◽  
Data Sets ◽  
Regression Equations ◽  
Total Iron Content ◽  
Data Set ◽  
X Ray ◽  
The Difference

The X-ray attenuation (Sedigraph) method for particle-size analysis is known to consistently estimate a finer size distribution than the pipette method. The objectives of this study were to compare the two methods, and to explore the reasons for their divergence. The methods are compared using two data sets from measurements made independently in two New Zealand laboratories, on two different sets of New Zealand soils, covering a range of textures and parent materials. The Sedigraph method gave systematically greater mass percentages at the four measurement diameters (20, 10, 5 and 2 �m). For one data set, the difference between clay (<2 �m) percentages from the two methods is shown to be positively correlated (R2 = 0.625) with total iron content of the sample, for all but one of the soils. This supports a novel hypothesis that the typically greater concentration of Fe (a strong X-ray absorber) in smaller size fractions is the major factor causing the difference. Regression equations are presented for converting the Sedigraph data to their pipette equivalents.

Charge Density of L-Alanyl-glycyl-L-alanine Based on X-Ray Data Collection Periods from 4 to 130 Hours

2007 ◽  
Vol 62 (5) ◽  
pp. 696-704 ◽  
Author(s):  
Diana Förster ◽  
Armin Wagner ◽  
Christian B. Hübschle ◽  
Carsten Paulmann ◽  
Peter Luger
Keyword(s):  
Synchrotron Radiation ◽  
Low Temperature ◽  
Charge Density ◽  
Data Sets ◽  
Data Set ◽  
X Ray ◽  
Atomic Properties ◽  
Multipole Refinement ◽  
Refinement Strategy ◽  
Experimental Charge Density

Abstract The charge density of the tripeptide L-alanyl-glycyl-L-alanine was determined from three X-ray data sets measured at different experimental setups and under different conditions. Two of the data sets were measured with synchrotron radiation (beamline F1 of Hasylab/DESY, Germany and beamline X10SA of SLS, Paul-Scherer-Institute, Switzerland) at temperatures around 100 K while a third data set was measured under home laboratory conditions (MoKα radiation) at a low temperature of 20 K. The multipole refinement strategy to derive the experimental charge density was the same in all cases, so that the obtained charge density properties could directly be compared. While the general analysis of the three data sets suggested a small preference for one of the synchrotron data sets (Hasylab F1), a comparison of topological and atomic properties gave in no case an indication for a preference of any of the three data sets. It follows that even the 4 h data set measured at the SLS performed equally well compared to the data sets of substantially longer exposure time.

scholarly journals Two decades of satellite observations of AOD over mainland China using ATSR-2, AATSR and MODIS/Terra: data set evaluation and large-scale patterns

2018 ◽  
Vol 18 (3) ◽  
pp. 1573-1592 ◽  
Author(s):  
Gerrit de Leeuw ◽  
Larisa Sogacheva ◽  
Edith Rodriguez ◽  
Konstantinos Kourtidis ◽  
Aristeidis K. Georgoulias ◽  
...  
Keyword(s):  
Time Series ◽  
European Space Agency ◽  
Mainland China ◽  
Satellite Observations ◽  
Data Sets ◽  
Data Set ◽  
Modis Aod ◽  
The Difference ◽  
Along Track ◽  
Aerosol Properties

Abstract. The retrieval of aerosol properties from satellite observations provides their spatial distribution over a wide area in cloud-free conditions. As such, they complement ground-based measurements by providing information over sparsely instrumented areas, albeit that significant differences may exist in both the type of information obtained and the temporal information from satellite and ground-based observations. In this paper, information from different types of satellite-based instruments is used to provide a 3-D climatology of aerosol properties over mainland China, i.e., vertical profiles of extinction coefficients from the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP), a lidar flying aboard the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) satellite and the column-integrated extinction (aerosol optical depth – AOD) available from three radiometers: the European Space Agency (ESA)'s Along-Track Scanning Radiometer version 2 (ATSR-2), Advanced Along-Track Scanning Radiometer (AATSR) (together referred to as ATSR) and NASA's Moderate Resolution Imaging Spectroradiometer (MODIS) aboard the Terra satellite, together spanning the period 1995–2015. AOD data are retrieved from ATSR using the ATSR dual view (ADV) v2.31 algorithm, while for MODIS Collection 6 (C6) the AOD data set is used that was obtained from merging the AODs obtained from the dark target (DT) and deep blue (DB) algorithms, further referred to as the DTDB merged AOD product. These data sets are validated and differences are compared using Aerosol Robotic Network (AERONET) version 2 L2.0 AOD data as reference. The results show that, over China, ATSR slightly underestimates the AOD and MODIS slightly overestimates the AOD. Consequently, ATSR AOD is overall lower than that from MODIS, and the difference increases with increasing AOD. The comparison also shows that neither of the ATSR and MODIS AOD data sets is better than the other one everywhere. However, ATSR ADV has limitations over bright surfaces which the MODIS DB was designed for. To allow for comparison of MODIS C6 results with previous analyses where MODIS Collection 5.1 (C5.1) data were used, also the difference between the C6 and C5.1 merged DTDB data sets from MODIS/Terra over China is briefly discussed. The AOD data sets show strong seasonal differences and the seasonal features vary with latitude and longitude across China. Two-decadal AOD time series, averaged over all of mainland China, are presented and briefly discussed. Using the 17 years of ATSR data as the basis and MODIS/Terra to follow the temporal evolution in recent years when the environmental satellite Envisat was lost requires a comparison of the data sets for the overlapping period to show their complementarity. ATSR precedes the MODIS time series between 1995 and 2000 and shows a distinct increase in the AOD over this period. The two data series show similar variations during the overlapping period between 2000 and 2011, with minima and maxima in the same years. MODIS extends this time series beyond the end of the Envisat period in 2012, showing decreasing AOD.

scholarly journals Quantifying instrument errors in macromolecular X-ray data sets

2010 ◽  
Vol 66 (6) ◽  
pp. 733-740 ◽  
Author(s):  
Kay Diederichs
Keyword(s):  
Data Reduction ◽  
Spindle Speed ◽  
Experimental Setup ◽  
Data Sets ◽  
Signal To Noise ◽  
Instrument Error ◽  
Acta Cryst ◽  
Data Set ◽  
X Ray ◽  
The Stability

An indicator which is calculated after the data reduction of a test data set may be used to estimate the (systematic) instrument error at a macromolecular X-ray source. The numerical value of the indicator is the highest signal-to-noise [I/σ(I)] value that the experimental setup can produce and its reciprocal is related to the lower limit of the mergingRfactor. In the context of this study, the stability of the experimental setup is influenced and characterized by the properties of the X-ray beam, shutter, goniometer, cryostream and detector, and also by the exposure time and spindle speed. Typical values of the indicator are given for data sets from the JCSG archive. Some sources of error are explored with the help of test calculations usingSIM_MX[Diederichs (2009),Acta Cryst.D65, 535–542]. One conclusion is that the accuracy of data at low resolution is usually limited by the experimental setup rather than by the crystal. It is also shown that the influence of vibrations and fluctuations may be mitigated by a reduction in spindle speed accompanied by stronger attenuation.

scholarly journals Evaluative application of UKCP09‐based downscaled future weather years to simulate overheating risk in typical English homes

2013 ◽  
Vol 31 (4) ◽  
pp. 231-252 ◽  
Author(s):  
Rajat Gupta ◽  
Matthew Gregg ◽  
Hu Du ◽  
Katie Williams
Keyword(s):  
Climate Change ◽  
Simulation Modelling ◽  
Simulation Software ◽  
Building Simulation ◽  
Future Research ◽  
Climate Projections ◽  
Data Sets ◽  
Data Set ◽  
Content Type ◽  
The Difference

PurposeTo critically compare three future weather year (FWY) downscaling approaches, based on the 2009 UK Climate Projections, used for climate change impact and adaptation analysis in building simulation software.Design/methodology/approachThe validity of these FWYs is assessed through dynamic building simulation modelling to project future overheating risk in typical English homes in 2050s and 2080s.FindingsThe modelling results show that the variation in overheating projections is far too significant to consider the tested FWY data sets equally suitable for the task.Research and practical implicationsIt is recommended that future research should consider harmonisation of the downscaling approaches so as to generate a unified data set of FWYs to be used for a given location and climate projection. If FWY are to be used in practice, live projects will need viable and reliable FWY on which to base their adaptation decisions. The difference between the data sets tested could potentially lead to different adaptation priorities specifically with regard to time series and adaptation phasing through the life of a building.Originality/valueThe paper investigates the different results derived from FWY application to building simulation. The outcome and implications are important considerations for research and practice involved in FWY data use in building simulation intended for climate change adaptation modelling.

Crystal and Molecular Structure of Thiocarbonyl-ethoxo(tetraphenylporphyrinato)ruthenium(II), [Ru(TPP)(CS)(HOC2H5)]. A Case of Centrosymmetric–Noncentrosymmetric Ambiguity

1997 ◽  
Vol 53 (5) ◽  
pp. 767-772 ◽  
Author(s):  
T. J. Bartczak ◽  
K. Rachlewicz ◽  
L. Latos-Grażynski
Keyword(s):  
Crystal And Molecular Structure ◽  
Bond Angle ◽  
Data Sets ◽  
Alpha Radiation ◽  
Data Set ◽  
Fourier Methods ◽  
Space Group ◽  
Space Groups ◽  
The Mean ◽  
Difference Fourier

[Ru(TPP)(CS)(EtOH)] crystallizes in the triclinic system. Crystal data: C47H34N4ORuS, M r = 803.91, a = 10.607 (3), b = 11.308 (5), c = 17.699 (2) Å, \alpha = 77.53 (2), \beta = 73.17 (1), \gamma = 69.85 (3)°, V = 1891.6 (10) Å3, P\overline 1 (C^{1}_{i}, no. 2), Z = 2, F(000) = 824, D x = 1.410, D m = 1.39 Mg m−3 (by flotation in aqueous KI), \mu(Mo K\alpha) = 0.512 mm−1, R = 0.094, wR = 0.098, S = 2.28 for 4610 independent reflections with F o > 5\sigma(F o ). A second data set was collected using Cu K\alpha radiation. The structure was refined by standard least-squares and difference-Fourier methods in space groups P1 and P\overline 1 using both the Mo K\alpha and Cu K\alpha data sets. Both data sets favor space group P\overline 1, the Mo data giving a slightly better result than the Cu data. The two independent Ru atoms lie on the inversion centers ½,0,0 and ½,½,½ of space group P\overline 1. Consequently, the two independent molecules have crystallographically imposed \overline 1 symmetry, the CS and EtOH axial groups are disordered and the RuN4 portions of the molecules are planar. The deviations from planarity of the porphyrinato core are very small. The Ru—C—S groups are essentially linear with an average Ru—C—S bond angle of 174 (1)°. The mean Ru—C(CS) and Ru—O (Et) bond lengths are 1.92 (4) and 2.15 (3) Å, respectively.

Combining cross-crystal averaging and MRSAD to phase a 4354-amino-acid structure

2016 ◽  
Vol 72 (2) ◽  
pp. 182-191
Author(s):  
Jason Nicholas Busby ◽  
J. Shaun Lott ◽  
Santosh Panjikar
Keyword(s):  
Radiation Damage ◽  
Model Building ◽  
Data Sets ◽  
Low Resolution ◽  
Data Set ◽  
C Protein ◽  
Large Size ◽  
Anomalous Signal ◽  
Difference Fourier ◽  
Combined Data

The B and C proteins from the ABC toxin complex ofYersinia entomophagaform a large heterodimer that cleaves and encapsulates the C-terminal toxin domain of the C protein. Determining the structure of the complex formed by B and the N-terminal region of C was challenging owing to its large size, the non-isomorphism of different crystals and their sensitivity to radiation damage. A native data set was collected to 2.5 Å resolution and a non-isomorphous Ta6Br12-derivative data set was collected that showed strong anomalous signal at low resolution. The tantalum-cluster sites could be found, but the anomalous signal did not extend to a high enough resolution to allow model building. Selenomethionine (SeMet)-derivatized protein crystals were produced, but the high number (60) of SeMet sites and the sensitivity of the crystals to radiation damage made phasing using the SAD or MAD methods difficult. Multiple SeMet data sets were combined to provide 30-fold multiplicity, and the low-resolution phase information from the Ta6Br12data set was transferred to this combined data set by cross-crystal averaging. This allowed the Se atoms to be located in an anomalous difference Fourier map; they were then used inAuto-Rickshawfor multiple rounds of autobuilding and MRSAD.

scholarly journals SCIAMACHY WFM-DOAS XCO<sub>2</sub>: comparison with CarbonTracker XCO<sub>2</sub> focusing on aerosols and thin clouds

2012 ◽  
Vol 5 (2) ◽  
pp. 2887-2931 ◽  
Author(s):  
J. Heymann ◽  
O. Schneising ◽  
M. Reuter ◽  
M. Buchwitz ◽  
V. V. Rozanov ◽  
...  
Keyword(s):  
Southern Hemisphere ◽  
Temporal Correlation ◽  
Anthropogenic Activity ◽  
Data Sets ◽  
Spatial Correlations ◽  
Data Set ◽  
Cloud Data ◽  
Temporal Correlations ◽  
Retrieval Errors ◽  
The Difference

Abstract. Carbon dioxide (CO2) is the most important greenhouse gas whose atmospheric loading has been significantly increased by anthropogenic activity leading to global warming. Accurate measurements and models are needed in order to reliably predict our future climate. This, however, has challenging requirements. Errors in measurements and models need to be identified and minimised. In this context, we present a comparison between satellite-derived column-averaged dry air mole fractions of CO2, denoted XCO2, retrieved from SCIAMACHY/ENVISAT using the WFM-DOAS algorithm, and output from NOAA's global CO2 modelling and assimilation system CarbonTracker. We investigate to what extent differences between these two data sets are influenced by systematic retrieval errors due to aerosols and unaccounted clouds. We analyse seven years of SCIAMACHY WFM-DOAS version 2.1 retrievals (WFMDv2.1) using the latest version of CarbonTracker (version 2010). We investigate to what extent the difference between SCIAMACHY and CarbonTracker XCO2 are temporally and spatially correlated with global aerosol and cloud data sets. For this purpose, we use a global aerosol data set generated within the European GEMS project, which is based on assimilated MODIS satellite data. For clouds, we use a data set derived from CALIOP/CALIPSO. We find significant correlations of the SCIAMACHY minus CarbonTracker XCO2 difference with thin clouds over the Southern Hemisphere. The maximum temporal correlation we find for Darwin, Australia (r2 = 54%). Large temporal correlations with thin clouds are also observed over other regions of the Southern Hemisphere (e.g. 43% for South America and 31% for South Africa). Over the Northern Hemisphere the temporal correlations are typically much lower. An exception is India, where large temporal correlations with clouds and aerosols have also been found. For all other regions the temporal correlations with aerosol are typically low. For the spatial correlations the picture is less clear. They are typically low for both aerosols and clouds, but dependent on region and season, they may exceed 30% (the maximum value of 46% has been found for Darwin during September to November). Overall we find that the presence of thin clouds can potentially explain a significant fraction of the difference between SCIAMACHY WFMDv2.1 XCO2 and CarbonTracker over the Southern Hemisphere. Aerosols appear to be less of a problem. Our study indicates that the quality of the satellite derived XCO2 will significantly benefit from a reduction of scattering related retrieval errors at least for the Southern Hemisphere.

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