Atomic temperature factor

The atomic temperature factors obtained after crystallographic refinement are significantly higher for cys530 than for the other site cysteine residues. This is also true when the Ni ion is compared to the Fe center. This may reflect conformational disorder due to the fact that the crystals are made of a mixture of different Ni states (40% Ni-A, 10% Ni-B, and 50% of an EPR-silent species) (52). 

The atomic temperature factor, or B factor, measures the dynamic disorder caused by the temperature-dependent vibration of the atom, as well as the static disorder resulting from subtle structural differences in different unit cells throughout the crystal. For a B factor of 15 A2, displacement of an atom from its equilibrium position is approximately 0.44 A, and it is as much as 0.87 A for a B factor of 60 A2. It is very important to inspect the B factors during any structural analysis a B factor of less than 30 A2 for a particular atom usually indicates confidence in its atomic position, but a B factor of higher than 60 A2 likely indicates that the atom is disordered. 

The Relation between the Atomic Temperature Factors and Lattice Dynamics... 

Extinction, which is the failure of the kinematic scattering theory (Ihki hki) is only a minor problem in X-ray diffraction. In neutron diffraction, extinction is serious and pervasive throughout the whole data, as shown by the examples in Thble 3.2. The best methods available for extinction correction require careful measurement of crystal dimensions. Although somewhat empirical, it has proved to be very effective [184, 185]. At least one, and sometimes six, additional extinction parameters, gis0 or gij, have to be added to the variable parameters. Uncertainty in the validity of these extinction parameters appears to have very little effect on atomic positional coordinates, but may influence the absolute values of the atomic temperature factors. This is important in charge density or electrostatic potential... 

The first sum extends over all space group symmetry operators 0, ts) composed of a rotation matrix and a translation vector tg. The second sum extends over all unique atoms i of the system. The quantity fi denotes the orthogonal coordinates of atom i in A. T is the 3x3 matrix that converts orthogonal (A) coordinates into fractional coordinates F is its transpose. Bi, qi are respectively the atomic temperature factor and occupancy for atom i. The atomic form factors /j(/i) are typically approximated by an expression consisting of several Gaussians and a constant [19]... 

We showed that an ensemble of eight lysozyme structures, comprising 19335 atoms, could reproduce the observed conformational flexibility of lysozyme in a way that was consistent with both the observed X-ray scattering data and standard requirements for a chemically reasonable stmcture. By using an ensemble we hoped to better reflect the anisotropy of the system without the need to introduce anisotropic atomic temperature factors (B factors). In this way the total number of parameters... 

Where fa is the atomic scattering factor defined for stationary atoms, B is the atomic temperature factor, (also called the Debye-Waller... 

The atomic temperature factor is related to the magnitude of the vibration of the atom concerned by the equation ... 

The effect of absorption on the reflection intensities is obviously to reduce them in the absence of a correction this would affect the estimation of individual atomic temperature factors in refinement. The absorption corrections applied to individual reflections are usually different from one to another. In the case where a single data set is made up of several crystals (because of radiation damage), each of variable shape, then the lack of an absorption correction will leave systematic errors in the data. Even when a single crystal is used for a complete native data set and an identically shaped and mounted crystal is used as the heavy atom derivative, the lack of an absorption correction can seriously affect the measured isomorphous or anomalous differences. 

By is usually known as the atomic temperature factor, given by Bi=8it Uf (A ), where Uf is the vibration mean-square amplitude of the atom. 

It is apparent that in all cases the tetrahedra are distorted. One type of distortion is exhibited by the Zn and Co compounds, in all cases showing the angle Xj-M-X larger than 109,5° and the angle X -M-X smaller than 109,5°. Examination of intermolecular approach distances and individual atom temperature factors in the case of the Cs ZnEr has shown that this distortion is... 

A phase transition probably to a superlattice structure has been observed for Hofmann-dahxn-type -toluidine clathrate at 200 K. Above this temperature the atomic temperature factors of the guest molecule increase steeply to suggest that the librational motion of the guest molecule is excited thermally. The details of the phase transition is still unknown, although it should be related to motion of the guest molecule. 

The be projection of poly(5,7-dodecadiinediol-l,12-bis-phenylurethane) is shown in figure 1. Although not indicated in this figure reasonable anisotropic temperature factors were obtained for all atoms. Hydrogen atom temperature factors were held isotropic. The final residual R=0.08. Standard deviations for bond angles were 1 degree while... 

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