scholarly journals B-factor accuracy in protein crystal structures

2022 ◽  
Vol 78 (1) ◽  
Author(s):  
Oliviero Carugo
Keyword(s):  
Low Temperature ◽  
Crystal Structures ◽  
Protein Dynamics ◽  
Diffraction Data ◽  
Large Scale ◽  
Crystal Defects ◽  
Protein Crystal ◽  
Computational Tools ◽  
Normal Probability ◽  
Quantitative Analyses

The accuracy of B factors in protein crystal structures has been determined by comparing the same atoms in numerous, independent crystal structures of Gallus gallus lysozyme. Both B-factor absolute differences and normal probability plots indicate that the estimated B-factor errors are quite large, close to 9 Å2 in ambient-temperature structures and to 6 Å2 in low-temperature structures, and surprisingly are comparable to values estimated two decades ago. It is well known that B factors are not due to local movements only but reflect several, additional factors from crystal defects, large-scale disorder, diffraction data quality etc. It therefore remains essential to normalize B factors when comparing different crystal structures, although it has clearly been shown that they provide useful information about protein dynamics. Improved, quantitative analyses of raw B factors require novel experimental and computational tools that are able to disaggregate local movements from other features and properties that affect B factors.

scholarly journals Structure determination from powder diffraction data

2007 ◽  
Vol 64 (1) ◽  
pp. 52-64 ◽  
Author(s):  
W. I. F. David ◽  
K. Shankland
Keyword(s):  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Optimization Methods ◽  
Protein Crystal ◽  
Powder Diffraction Data ◽  
Structure Solution ◽  
Combined Use ◽  
Complementary Techniques

Advances made over the past decade in structure determination from powder diffraction data are reviewed with particular emphasis on algorithmic developments and the successes and limitations of the technique. While global optimization methods have been successful in the solution of molecular crystal structures, new methods are required to make the solution of inorganic crystal structures more routine. The use of complementary techniques such as NMR to assist structure solution is discussed and the potential for the combined use of X-ray and neutron diffraction data for structure verification is explored. Structures that have proved difficult to solve from powder diffraction data are reviewed and the limitations of structure determination from powder diffraction data are discussed. Furthermore, the prospects of solving small protein crystal structures over the next decade are assessed.

Waters in room temperature and cryo protein crystal structures

2016 ◽  
Vol 231 (11) ◽  
Author(s):  
Oliviero Carugo
Keyword(s):  
Low Temperature ◽  
Crystal Structures ◽  
Room Temperature ◽  
Protein Structures ◽  
Water Structure ◽  
Protein Crystal ◽  
Quality Data ◽  
Water Molecules ◽  
Data Sets ◽  
Density Maps

AbstractSince it has been observed that low temperature protein crystal structures may differ from room temperature structures, it is necessary to compare systematically the protein hydration structure in low and room protein crystal structures. High quality data sets of protein structures were built in an extremely rigorous manner and crystal symmetry was included in the identification of four types of water molecules (buried in the protein core, deeply inserted into crevices at the protein surface, first and second hydration layers). More water molecules are observed at low temperature only if the resolution is better than 2.1–2.3 Å. At worse resolution, temperature does not play any role. The numerous water molecules that become detectable at low temperature and at higher resolution are more mobile, relative to the protein average flexibility. Despite that, the occupancy does not depend on temperature. It can be hypothesized that water structure and around proteins and hydrogen bond network do not depend on the temperature, at least in the temperature range examined here. At low temperature more water molecules are detected because the average flexibility of all the atoms decreases, so that also water molecules that are considerably more mobile than the average atoms become observable in the electron density maps.

Crystal structures of room- and low-temperature phases in oxyfluoride (NH4)2KWO3F3

2007 ◽  
Vol 22 (3) ◽  
pp. 227-230 ◽  
Author(s):  
M. S. Molokeev ◽  
A. D. Vasiliev ◽  
A. G. Kocharova
Keyword(s):  
Low Temperature ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Room Temperature ◽  
Monoclinic Phase ◽  
Temperature Structure ◽  
Powder Diffraction Data ◽  
Space Group ◽  
X Ray

Crystal structures of (NH4)2KWO3F3 at 298 K and 113 K were solved from X-ray powder diffraction data and refined by the Rietveld technique. The compound is isostructural with elpasolite K2NaAlF6 at room temperature with space group Fm-3m, a=8.95850(5) Å, V=718.961(7) Å3, Z=4, Dx=3.363 g/cm3, and MW=364.02. The structure was refined over 18 parameters to Rwp=12.6%, Rp=10.9%, Rexp=5.03%, and RB=3.27% from 40 independent reflections. (NH4)2KWO3F3 was transformed upon cooling to a ferroelastic monoclinic phase with space group P21/n, a′=6.3072(3) Å, b′=6.3028(3) Å, c′=8.9882(3) Å, β′=90.242(2)°, V=357.30(3) Å3, Z=2, and Dx=3.383 g/cm3. The low-temperature structure at 113 K was refined over 28 parameters to Rwp=20.9%, Rp=21.3%, Rexp=12.5%, and RB=6.93% from 453 independent reflections.

Crystal structures of hydrofluorocarbons from powder X-ray diffraction data: HFC-134a and HFC-152a

2002 ◽  
Vol 217 (7-8) ◽  
Author(s):  
M. Brunelli ◽  
A. N. Fitch
Keyword(s):  
High Resolution ◽  
Low Temperature ◽  
Crystal Structures ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
Melting Points ◽  
X Ray ◽  
Hfc 134A ◽  
Hfc 152A

AbstractHigh-resolution powder X-ray diffraction measurements have been used to determine the low-temperature crystal structures of the hydrofluorocarbons 1,1,1,2-tetrafluoroethane (HFC-134a) and 1,2-difluoroethane (HFC-152a). Below their melting points both compounds form body-centred-cubic orientationally-disordered phases with a = 5.7606(2) Å for HFC-134a and

The Imaging of Crystal Structures and Crystal Defects

1978 ◽  
Vol 36 (3) ◽  
pp. 207-217
Author(s):  
J.M. Cowley
Keyword(s):  
Electron Microscope ◽  
Crystal Structures ◽  
Phase Contrast ◽  
Crystal Defects ◽  
Atom Density ◽  
Lack Of Information ◽  
Spatial Frequencies

The problem of "understandinq" electron microscope imaqes becomes more acute as the resolution is improved. The naive interpretation of an imaqe as representinq the projection of an atom density becomes less and less appropriate. We are increasinqly forced to face the complexities of coherent imaqinq of what are essentially phase objects. Most electron microscopists are now aware that, for very thin weakly scatterinq objects such as thin unstained bioloqical specimens, hiqh resolution imaqes are best obtained near the optimum defocus, as prescribed by Scherzer, where the phase contrast imaqe qives a qood representation of the projected potential, apart from a lack of information on the lower spatial frequencies. But phase contrast imaqinq is never simple except in idealized limitinq cases.

scholarly journals Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches

2021 ◽  
Author(s):  
Mehdi A. Beniddir ◽  
Kyo Bin Kang ◽  
Grégory Genta-Jouve ◽  
Florian Huber ◽  
Simon Rogers ◽  
...  
Keyword(s):  
Natural Product ◽  
Large Scale ◽  
Scale Analysis ◽  
Computational Tools ◽  
Natural Product Discovery ◽  
Large Scale Analysis ◽  
Metabolite Annotation

This review highlights the key computational tools and emerging strategies for metabolite annotation, and discusses how these advances will enable integrated large-scale analysis to accelerate natural product discovery.

scholarly journals Sustainable Large-Scale Aquaculture of the Northern Hemisphere Sea Lettuce, Ulva fenestrata, in an Off-Shore Seafarm

2021 ◽  
Vol 9 (6) ◽  
pp. 615
Author(s):  
Sophie Steinhagen ◽  
Swantje Enge ◽  
Karin Larsson ◽  
Joakim Olsson ◽  
Göran M. Nylund ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Low Temperature ◽  
Northern Hemisphere ◽  
Biochemical Composition ◽  
Large Scale ◽  
Biomass Yield ◽  
Phenolic Content ◽  
Seedling Density ◽  
Ulva Fenestrata ◽  
High Nutrient

The growing world population demands an increase in sustainable resources for biorefining. The opening of new farm grounds and the cultivation of extractive species, such as marine seaweeds, increases worldwide, aiming to provide renewable biomass for food and non-food applications. The potential for European large-scale open ocean farming of the commercial green seaweed crop Ulva is not yet fully realized. Here we conducted manipulative cultivation experiments in order to investigate the effects of hatchery temperature (10 and 15 °C), nutrient addition (PES and 3xPES) and swarmer density (500 and 10,000 swarmers ml−1) on the biomass yield and biochemical composition (fatty acid, protein, carbohydrate, pigment and phenolic content) of off-shore cultivated Ulva fenestrata in a Swedish seafarm. High seedling densities were optimal for the growth of this northern hemisphere crop strain and significantly increased the mean biomass yield by ~84% compared to low seedling densities. Variations of nutrients or changes in temperature levels during the hatchery phase were not necessary to increase the subsequent growth in an open-water seafarm, however effects of the factors on the thallus habitus (thallus length/width) were observed. We found no significant effect of the environmental factors applied in the hatchery on the total fatty acid or crude protein content in the off-shore cultivated Ulva. However, low seedling density and low temperature increased the total carbohydrate content and furthermore, high temperature in combination with high nutrient levels decreased the pigment content (chlorophyll a, b, carotenoids). Low temperature in combination with high nutrient levels increased the phenolic content. Our study confirms the successful and sustainable potential for large-scale off-shore cultivation of the Scandinavian crop U. fenestrata. We conclude that high seedling density in the hatchery is most important for increasing the total biomass yield of sea-farmed U. fenestrata, and that changing temperature or addition of nutrients overall does not have a large effect on the biochemical composition. To summarize, our study contributes novel insights into the large-scale off-shore cultivation potential of northern hemisphere U. fenestrata and underpins suitable pre-treatments during the hatchery phase of seedlings to facilitate a successful and cost-efficient large-scale rope cultivation.

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