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 Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca2+-calmodulin

2016 ◽  
Vol 72 (1) ◽  
pp. 83-92 ◽  
Author(s):  
Jiusheng Lin ◽  
Henry van den Bedem ◽  
Axel T. Brunger ◽  
Mark A. Wilson
Keyword(s):  
Crystal Structures ◽  
Electron Density ◽  
Full Range ◽  
Binding Pocket ◽  
Data Set ◽  
Conformational Substates ◽  
Density Maps ◽  
Hydrophobic Binding ◽  
Ef Hands ◽  
Critical Regions

Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca2+-CaM, but no assignment of these features has been made. In addition, Ca2+-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 Å resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca2+-CaM. Density-modified electron-density maps enabled the accurate assignment of Ca2+-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using low-contour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca2+-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca2+-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca2+-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal.

Enhanced electron-density envelopes by extended solvent definition

1998 ◽  
Vol 54 (3) ◽  
pp. 461-466 ◽  
Author(s):  
Nick Blom ◽  
Jurgen Sygush
Keyword(s):  
Amino Acid ◽  
Electron Density ◽  
Considerable Improvement ◽  
Amino Acid Sequences ◽  
Water Molecules ◽  
E Coli ◽  
Density Maps ◽  
Weak Electron

Extended delineation of water molecules, monitored using R free values, afforded considerable improvement in quality of electron-density maps for structure determination of mammalian class I and E. coli class II aldolases. Augmented solvent definition results in an additional decrease in R free values of 3–4% and is reflected in significantly enhanced electron-density envelopes enabling tracing of amino-acid sequences through regions of otherwise discontinuous or weak electron density.

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.

scholarly journals High-resolution neutron and X-ray diffraction room-temperature studies of an H-FABP–oleic acid complex: study of the internal water cluster and ligand binding by a transferred multipolar electron-density distribution

IUCrJ ◽  
2016 ◽  
Vol 3 (2) ◽  
pp. 115-126 ◽  
Author(s):  
E. I. Howard ◽  
B. Guillot ◽  
M. P. Blakeley ◽  
M. Haertlein ◽  
M. Moulin ◽  
...  
Keyword(s):  
Oleic Acid ◽  
Fatty Acid ◽  
High Resolution ◽  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Room Temperature ◽  
Water Molecules ◽  
X Ray

Crystal diffraction data of heart fatty acid binding protein (H-FABP) in complex with oleic acid were measured at room temperature with high-resolution X-ray and neutron protein crystallography (0.98 and 1.90 Å resolution, respectively). These data provided very detailed information about the cluster of water molecules and the bound oleic acid in the H-FABP large internal cavity. The jointly refined X-ray/neutron structure of H-FABP was complemented by a transferred multipolar electron-density distribution using the parameters of the ELMAMII library. The resulting electron density allowed a precise determination of the electrostatic potential in the fatty acid (FA) binding pocket. Bader's quantum theory of atoms in molecules was then used to study interactions involving the internal water molecules, the FA and the protein. This approach showed H...H contacts of the FA with highly conserved hydrophobic residues known to play a role in the stabilization of long-chain FAs in the binding cavity. The determination of water hydrogen (deuterium) positions allowed the analysis of the orientation and electrostatic properties of the water molecules in the very ordered cluster. As a result, a significant alignment of the permanent dipoles of the water molecules with the protein electrostatic field was observed. This can be related to the dielectric properties of hydration layers around proteins, where the shielding of electrostatic interactions depends directly on the rotational degrees of freedom of the water molecules in the interface.

scholarly journals Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Monarin Uervirojnangkoorn ◽  
Oliver B Zeldin ◽  
Artem Y Lyubimov ◽  
Johan Hattne ◽  
Aaron S Brewster ◽  
...  
Keyword(s):  
Data Processing ◽  
Diffraction Data ◽  
Free Electron ◽  
Biological Systems ◽  
Processing System ◽  
Data Set ◽  
X Ray ◽  
Density Maps ◽  
Beam Parameters

There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.

Mapping lipid and detergent molecules at the surface of membrane proteins

2011 ◽  
Vol 39 (3) ◽  
pp. 775-779 ◽  
Author(s):  
Richard J. Cogdell ◽  
Alastair T. Gardiner ◽  
Aleksander W. Roszak ◽  
Sigitas Stončius ◽  
Pavel Kočovský ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Crystal Structures ◽  
Present Article ◽  
Electron Density ◽  
Rhodobacter Sphaeroides ◽  
Binding Sites ◽  
Heavy Atom ◽  
Hydrophobic Surface ◽  
Density Maps ◽  
Blastochloris Viridis

Electron-density maps for the crystal structures of membrane proteins often show features suggesting binding of lipids and/or detergent molecules on the hydrophobic surface, but usually it is difficult to identify the bound molecules. In our studies, heavy-atom-labelled phospholipids and detergents have been used to unequivocally identify these binding sites at the surfaces of test membrane proteins, the reaction centres from Rhodobacter sphaeroides and Blastochloris viridis. The generality of this method is discussed in the present article.

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.

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