Reliability of atomic displacement parameters in protein crystal structures

1999 ◽  
Vol 55 (2) ◽  
pp. 473-478 ◽  
Author(s):  
Oliviero Carugo ◽  
Patrick Argos
Keyword(s):  
Protein Structures ◽  
Atomic Displacement ◽  
Protein Crystal ◽  
Nonlinear Dependence ◽  
Standard Errors ◽  
Unexpected Result ◽  
Protein Chain ◽  
Space Groups ◽  
Structure Determinations ◽  
Atomic Displacement Parameters

Mean standard errors in atomic displacement parameters (ADPs) resulting from protein crystal structure determinations are estimated by comparing the ADPs of protein-chain pairs of identical sequence within the same crystal or within different crystals displaying the same or different space groups. The estimated ADP standard errors increase nearly linearly as the resolution decreases – an unexpected result given the nonlinear dependence of the resolution on the amount of diffraction data. The estimated ADP standard errors are larger for side-chain and solvent-exposed atoms than for main-chain and buried atoms and, surprisingly, are also larger for residues in the helical secondary structure relative to other local backbone conformations. The results allow an estimate of the influence of crystallographic refinement restraints on ADP standard errors. Such corrections should be applied when comparing different protein structures.

scholarly journals Room-temperature ultrahigh-resolution time-of-flight neutron and X-ray diffraction studies of H/D-exchanged crambin

2012 ◽  
Vol 68 (2) ◽  
pp. 119-123 ◽  
Author(s):  
Julian C.-H. Chen ◽  
Zoë Fisher ◽  
Andrey Y. Kovalevsky ◽  
Marat Mustyakimov ◽  
B. Leif Hanson ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Room Temperature ◽  
Protein Structures ◽  
Atomic Displacement ◽  
Protein Crystal ◽  
X Ray Diffraction ◽  
Resolution Time ◽  
X Ray ◽  
Two Temperatures ◽  
Atomic Displacement Parameters

The room-temperature (RT) X-ray structure of H/D-exchanged crambin is reported at 0.85 Å resolution. As one of the very few proteins refined with anisotropic atomic displacement parameters at two temperatures, the dynamics of atoms in the RT and 100 K structures are compared. Neutron diffraction data from an H/D-exchanged crambin crystal collected at the Protein Crystallography Station (PCS) showed diffraction beyond 1.1 Å resolution. This is the highest resolution neutron diffraction reported to date for a protein crystal and will reveal important details of the anisotropic motions of H and D atoms in protein structures.

scholarly journals Which metal or ion? Identification of metals and ions in protein structures

2014 ◽  
Vol 70 (a1) ◽  
pp. C1484-C1484
Author(s):  
Jan Dohnalek
Keyword(s):  
Electron Density ◽  
Metal Binding ◽  
Active Sites ◽  
Protein Structures ◽  
Atomic Displacement ◽  
Large Set ◽  
Protein Chain ◽  
Trace Impurities ◽  
X Ray ◽  
Atomic Displacement Parameters

Identification of ligands in single crystals of biomolecules is often uneasy. The target molecules undergo expression, purification, and special pre-crystallization treatment and even trace impurities in known chemicals become a source of potential ligands. The final "binders" belong to a large set of both natural cofactors and chemicals encountered before the diffraction experiment. Some promiscuous metal binding sites can bind different types of metals of the fourth period and activity towards the same substrate can be measured with different divalent metals in active sites of nucleases, anhydrolases, etc. Therefore, 1) Not all structures have correct ions; 2) Ion identification in all structures requires high attention, especially in metal-dependent proteins. To date 98% of X-ray structures in the PDB have the high diffraction limit of 1.2 Å or worse. Thus we must rely on other indicators as for the ion type than just the height of electron density because our data often provide an accurate picture of a mixture of states. Therefore, essential determinants (relative heights of unbiased electron density maxima, anomalous signal, the shortest interatomic distances, stability of atoms in refinement, nature of coordinating atoms) must be distinguished from marginal factors which can be smeared by worse data quality, resolution limits, position in protein chain or local disorder (atomic displacement parameters, occurrence of longer coordination distances, missing vertices of the first coordination sphere). We have applied the described approach to identify cations, such as Cu2+, Mn2+, Zn2+, Ni2+, Ca2+, Mg2+, Na+ and other ionic ligands, for instance Cl-, PO43-, SO42- [1]. The available tools for identification of metals/ions also include statistics on coordination and bonding distances [2], absorption edge detection and fluorescence [1] or microbeam proton induced X-ray emission [3]. The work was supported by MEYS CR (EE2.3.30.0029) and BIOCEV (CZ.1.05/1.1.00/02.0109).

scholarly journals How anisotropic and isotropic atomic displacement parameters monitor protein covalent bonds rigidity: isotropic B-factors underestimate bond rigidity

Amino Acids ◽  
2021 ◽  
Author(s):  
Oliviero Carugo
Keyword(s):  
Protein Structures ◽  
Covalent Bond ◽  
Atomic Displacement ◽  
High Quality ◽  
Covalent Bonds ◽  
The Mean ◽  
The Difference ◽  
Atomic Displacement Parameters ◽  
Protein Covalent ◽  
Better Than

AbstractUnder the assumption that covalent bonds are rigid, it is possible to compare the estimations of rigidity based on anisotropic and isotropic B-factors. This is done by computing the difference of the mean-square displacements (Delta-u) of atoms A and Z along the covalent bond A–Z, which must be close to zero for a rigid bond. The analysis of a high-quality set of protein structures, refined at a resolution better than (or equal to) 0.8 Angstroms, showed that Delta-u is significantly close to zero when anisotropic B-factors are used, with an average 60% Delta-u reduction. This reduction is larger for larger B-factors and this suggests that care should be taken in data-mining procedures that involve isotropic B-factors, especially at lower resolution, when anisotropic B-factors cannot be determined and when the average B-factor increases.

scholarly journals Exploring ligand dynamics in protein crystal structures with ensemble refinement

2021 ◽  
Vol 77 (8) ◽  
Author(s):  
Octav Caldararu ◽  
Vilhelm Ekberg ◽  
Derek T. Logan ◽  
Esko Oksanen ◽  
Ulf Ryde
Keyword(s):  
Crystal Structures ◽  
Automatic Generation ◽  
Atomic Displacement ◽  
Point Of View ◽  
Protein Crystal ◽  
Statistical Point ◽  
X Ray Crystallography ◽  
Conformational Diversity ◽  
Atomic Displacement Parameters ◽  
Dynamics Simulations

Understanding the dynamics of ligands bound to proteins is an important task in medicinal chemistry and drug design. However, the dominant technique for determining protein–ligand structures, X-ray crystallography, does not fully account for dynamics and cannot accurately describe the movements of ligands in protein binding sites. In this article, an alternative method, ensemble refinement, is used on six protein–ligand complexes with the aim of understanding the conformational diversity of ligands in protein crystal structures. The results show that ensemble refinement sometimes indicates that the flexibility of parts of the ligand and some protein side chains is larger than that which can be described by a single conformation and atomic displacement parameters. However, since the electron-density maps are comparable and R free values are slightly increased, the original crystal structure is still a better model from a statistical point of view. On the other hand, it is shown that molecular-dynamics simulations and automatic generation of alternative conformations in crystallographic refinement confirm that the flexibility of these groups is larger than is observed in standard refinement. Moreover, the flexible groups in ensemble refinement coincide with groups that give high atomic displacement parameters or non-unity occupancy if optimized in standard refinement. Therefore, the conformational diversity indicated by ensemble refinement seems to be qualitatively correct, indicating that ensemble refinement can be an important complement to standard crystallographic refinement as a tool to discover which parts of crystal structures may show extensive flexibility and therefore are poorly described by a single conformation. However, the diversity of the ensembles is often exaggerated (probably partly owing to the rather poor force field employed) and the ensembles should not be trusted in detail.

scholarly journals Crystal Structure of Moganite and Its Anisotropic Atomic Displacement Parameters Determined by Synchrotron X-ray Diffraction and X-ray/Neutron Pair Distribution Function Analyses

Minerals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 272
Author(s):  
Seungyeol Lee ◽  
Huifang Xu ◽  
Hongwu Xu ◽  
Joerg Neuefeind
Keyword(s):  
Crystal Structure ◽  
Distribution Function ◽  
Single Crystal ◽  
Pair Distribution Function ◽  
Atomic Displacement ◽  
Single Crystal Xrd ◽  
X Ray Diffraction ◽  
X Ray ◽  
Neutron Pair ◽  
Atomic Displacement Parameters

The crystal structure of moganite from the Mogán formation on Gran Canaria has been re-investigated using high-resolution synchrotron X-ray diffraction (XRD) and X-ray/neutron pair distribution function (PDF) analyses. Our study for the first time reports the anisotropic atomic displacement parameters (ADPs) of a natural moganite. Rietveld analysis of synchrotron XRD data determined the crystal structure of moganite with the space group I2/a. The refined unit-cell parameters are a = 8.7363(8), b = 4.8688(5), c = 10.7203(9) Å, and β = 90.212(4)°. The ADPs of Si and O in moganite were obtained from X-ray and neutron PDF analyses. The shapes and orientations of the anisotropic ellipsoids determined from X-ray and neutron measurements are similar. The anisotropic ellipsoids for O extend along planes perpendicular to the Si-Si axis of corner-sharing SiO4 tetrahedra, suggesting precession-like movement. Neutron PDF result confirms the occurrence of OH over some of the tetrahedral sites. We postulate that moganite nanomineral is stable with respect to quartz in hypersaline water. The ADPs of moganite show a similar trend as those of quartz determined by single-crystal XRD. In short, the combined methods can provide high-quality structural parameters of moganite nanomineral, including its ADPs and extra OH position at the surface. This approach can be used as an alternative means for solving the structures of crystals that are not large enough for single-crystal XRD measurements, such as fine-grained and nanocrystalline minerals formed in various geological environments.

scholarly journals Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters

2021 ◽  
Vol 8 (4) ◽  
pp. 044701
Author(s):  
Zhen Su ◽  
Medhanjali Dasgupta ◽  
Frédéric Poitevin ◽  
Irimpan I. Mathews ◽  
Henry van den Bedem ◽  
...  
Keyword(s):  
Diffuse Scattering ◽  
Atomic Displacement ◽  
Potential Utility ◽  
X Ray ◽  
Protein X ◽  
Atomic Displacement Parameters

Incommensurate modulation of calcium barium niobate (CBN28 and Ce:CBN28)

2012 ◽  
Vol 68 (2) ◽  
pp. 101-106 ◽  
Author(s):  
Heribert A. Graetsch ◽  
Chandra Shekhar Pandey ◽  
Jürgen Schreuer ◽  
Manfred Burianek ◽  
Manfred Mühlberg
Keyword(s):  
Crystal Structures ◽  
Tungsten Bronze ◽  
Atomic Displacement ◽  
Type Structure ◽  
Formula Unit ◽  
Tetragonal Tungsten Bronze ◽  
First Order ◽  
Oxygen Coordination ◽  
Incommensurate Modulation ◽  
Atomic Displacement Parameters

The incommensurately modulated crystal structures of Ca0.28Ba0.72Nb2O6 (CBN28) and Ce0.02Ca0.25Ba0.72Nb2O6 (Ce:CBN28) were refined in the supercentred setting X4bm(AA0,−AA0) of the 3 + 2-dimensional superspace group P4bm(aa½,−aa½). Both compounds are isostructural with a tetragonal tungsten bronze-type structure. The modulation of CBN28 consists of a wavy distribution of Ba and Ca atoms as well as vacancies on the incompletely occupied Me2 site with 15-fold oxygen coordination. The occupational modulation is coupled with a modulation of the atomic displacement parameters and a very weak modulation of the positional parameters of Me2. The surrounding O atoms show strong displacive modulations with amplitudes up to ca 0.2 Å owing to the cooperative tilting of the rigid NbO6 octahedra. The Me1 site with 12-fold coordination and Nb atoms are hardly affected by the modulations. Only first-order satellites were observed and the modulations are described by first-order harmonics. In Ce:CBN28 cerium appears to be located on both the Me2 and Me1 sites. Wavevectors and structural modulations are only weakly modified upon substitutional incorporation of 0.02 cerium per formula unit of calcium.

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