Home | About | Journals | Submit | Contact Us | Français |

**|**Acta Crystallogr A**|**PMC3211245

Formats

Article sections

- Abstract
- 1. The origin of B eq
- 2. An alternative to B eq
- 3. Empirical comparison of anisotropic and isotropic refinement at atomic resolution
- 4. Application of B est to the identification of TLS groups based on analysis of an isotropic model
- 5. Concluding remarks
- References

Authors

Related links

Acta Crystallogr A. 2011 November 1; 67(Pt 6): 512–516.

Published online 2011 October 13. doi: 10.1107/S0108767311034350

PMCID: PMC3211245

Correspondence e-mail: ude.notgnihsaw.u@ttirrem

Received 2011 July 29; Accepted 2011 August 21.

Copyright © International Union of Crystallography 2011

Crystallographic structural models for macromolecules have typically included an isotropic displacement parameter *B*
_{iso} for each atom. In cases where the structural model instead includes anisotropic displacement parameters *U*
^{ij}, the derived quantity *B*
_{eq} can be substituted for *B*
_{iso} for many purposes. *B*
_{eq} is not, however, the best predictor of the value *B*
_{iso} that would hypothetically have been obtained by direct refinement of an isotropic model. A new entity *B*
_{est} is proposed that represents an estimate for *B*
_{iso} that minimizes the Kullback–Leibler divergence from a paired anisotropic model. In general *B*
_{est}/*B*
_{eq} < 1, with the difference between the two values becoming larger for atoms that are more anisotropic. Although this difference does not affect direct refinement of either isotropic or anisotropic models, it is relevant to any analysis that compares isotropic and anisotropic models of the same underlying structure. In particular, it may lead to improved selection of multi-group TLS models based on analysis of an initial isotropic refinement.

Two forms of atomic displacement parameters (ADPs) are commonly used in crystallographic models. Models refined against atomic-resolution data usually include a symmetric tensor **U** for each atom that describes anisotropic displacement. Models refined at lower resolution usually include instead an isotropic term *B*
_{iso} for each atom. Both the isotropic and anisotropic ADPs describe a three-dimensional Gaussian probability density function centered on the mean position of the corresponding atom. Because crystals of macromolecules typically diffract only to modest resolution, the use of *B*
_{iso} has been particularly common in structural models for macromolecules. Indeed, the standard ATOM record for structures archived in the Protein Data Bank (PDB) contains a field for a single ‘Temperature factor’ (Berman *et al.*, 2007 ), and many software tools that manipulate PDB files expect an isotropic ADP to be provided here.

The choice to use isotropic ADPs in macromolecular crystallography is a concession to the limited number of Bragg reflections available at lower resolution; only four parameters per atom [ are required for a model with isotropic ADPs as opposed to nine parameters per atom for a model with anisotropic ADPs. It is not driven by an expectation that macromolecular crystals exhibit less anisotropy. On the contrary, the inherent flexibility of macromolecules combined with the high solvent content and relatively loose lattice packing they exhibit when crystallized leads to substantial atomic anisotropy (Hinsen, 2008 ). This is borne out experimentally both by refinement of anisotropic ADPs for the small fraction of protein structures that diffract to true atomic resolution (Schneider, 1996 ; Merritt, 1999*b*
) and by the improved *R*-factors obtained even for low-resolution structures when relatively simple descriptions of bulk anisotropy are added to the model (Merritt, 2011 ). Thus it is becoming standard practice in protein crystallography to include an explicit model for bulk anisotropic displacements (Zucker *et al.*, 2010 ). The most common approach is to treat segments of the protein as approximately rigid groups exhibiting concerted displacements described by the translation/libration/screw (TLS) formalism (Trueblood, 1978 ; Howlin *et al.*, 1989 ; Winn *et al.*, 2001 ; Painter & Merritt, 2006 ). A second approach is to model concerted atomic displacements as arising from normal mode vibrations identified by an elastic network model (Poon *et al.*, 2007 ). In both approaches these bulk models are applied to generate conventional anisotropic ADP descriptions for each atom, which are in turn used to calculate the gradients that drive crystallographic refinement (Winn *et al.*, 2001 ; Chen *et al.*, 2007 ). The individual anisotropic ADPs derived in this way are Gaussian approximations to the non-Gaussian distributions described by the TLS or normal mode displacements, an approximation that is strictly valid only in the limiting case of infinitesimal displacement amplitude.

The output from refining this sort of model thus consists of direct estimates for the atomic positional coordinates and for the bulk displacement parameters. From these can be derived estimates of per-atom anisotropic Gaussian displacements. As in the case of refining a model at atomic resolution with anisotropic Gaussian ADPs for each atom, there is no direct refinement of a quantity equivalent to *B*
_{iso}. Nevertheless, as noted above, some software expects to have available a value representing the isotropic displacement of each atom. The quantity recommended for this purpose by the International Union of Crystallography (IUCr) (IUCr Commission on Journals, 1986 ) is

where **U** is the conventional symmetric tensor describing the displacement of that atom as an anisotropic three-dimensional Gaussian in Cartesian coordinates (Hamilton, 1959 ; Trueblood *et al.*, 1996 ). The physical interpretation of *B*
_{eq} is the mean-square displacement averaged over all directions. This is appropriate for the generation of figures that use a mean-square displacement isosurface as a visual cue for atomic displacement, *e.g.*
*ORTEP* (Burnett & Johnson, 1996 ). *B*
_{eq} is also adequate for qualitative evaluation of the relative vibrational motion of various parts of a structure. But it is not necessarily the best choice for other quantitative purposes. In particular, it is not the best estimate of the isotropic ADP *B*
_{iso} that would be obtained through direct refinement, as will be shown in this paper.

This distinction becomes important when an anisotropic model, for example a specific set of groups to be described by TLS, is chosen based on an existing model that was refined isotropically. In this case one wants to select from among many possible alternative anisotropic models the one model that makes the observed set of *B*
_{iso} values most likely. Thus a better estimator for *B*
_{iso} may lead to improved model selection.

Consider two possible models for the scattering contribution of a particular atom, the first containing an anisotropic description **U** of displacement about its mean position, the second containing an isotropic description **V** of displacement about that same mean position. In standard crystallographic treatment both the isotropic and the anisotropic descriptions are Gaussian approximations to the true atomic displacement underlying the experimentally observed scattering. Under these conditions the agreement between the two models may be quantified using the symmetric form of the Kullback–Leibler divergence for the corresponding probability density functions (Kullback & Leibler, 1951 ). Because **U** and **V** are Gaussian distributions centered at the origin, the symmetric form of their Kullback–Leibler divergence may be expressed (Murshudov *et al.*, 2011 ) as

= 0 if the two models are identical; otherwise > 0. We will explore the hypothesis that, given a set of refined values for the anisotropic ADPs *U*
^{ij}, the best predictor of the refined isotropic ADP *B*
_{iso} is that value *B*
_{est} which minimizes . In other words, we expect refinement of the isotropic model to converge to a state that minimizes disagreement with the anisotropic model.

Since **V** is isotropic we do not care about the orientation of **U** and can therefore rotate it to yield the convenient form

where , , are the eigenvalues of the original symmetric tensor. An equivalently convenient tensor form describing **V** in the same units as **U** is given by

where the scalar value = .

The minimum of is found by setting

which yields

and thus the desired entity

In the limiting case that **U** is isotropic, = = and = . In the general case, < . As **U** becomes increasingly anisotropic, the ratio of *B*
_{est} to *B*
_{eq} decreases (Fig. 1 ).

The atomic anisotropy for an atom described by ADP tensor **U** is defined as the ratio of the minimum eigenvalue of **U** to the maximum eigenvalue of **U**. For an isotropic atom, = 1. The mean anisotropy of atoms in individual macromolecular crystal structures refined at atomic resolution lies broadly in the range 0.4–0.6, with atoms in the structure exhibiting a roughly Gaussian distribution about that mean (Zucker *et al.*, 2010 ). Estimates for *B*
_{iso} made using *B*
_{est} rather than *B*
_{eq} will therefore be significantly smaller for most atoms in such structures. As an empirical test of whether *B*
_{est} is in fact a more accurate predictor, 15 high-resolution structures were selected as a test set (Table 1 ). These structures were chosen to span a range of mean anisotropy from 0.353 to 0.592. Thirteen of the structures were originally refined using *SHELXL97* (Sheldrick & Schneider, 1997 ), two (3cnj, 3lvc) were refined using *phenix.refine* (Adams *et al.*, 2010 ).

Coordinates and observed structure factors for each structure in the test set were obtained from the Protein Data Bank. Structure factors were converted from intensities to amplitudes if necessary. Each structure was then subjected to 15 cycles of isotropic refinement using *REFMAC* version 5.6.0095, starting from the original positional coordinates and the isotropic *B* factor ( as given in the ATOM records of the corresponding PDB file. To minimize shifts in the positional coordinates during refinement, interatomic distances were strongly restrained to their initial values *via* the command ‘RIDG DIST SIGM 0.00001’. H atoms were added in riding positions. All other refinement parameters were left at default values.

A modified version of the program *coruij* (Merritt, 1999*a*
) was used to compare the ATOM and ANISOU records from the original anisotropic model with the ATOM records in the refined isotropic model. The program verifies that the positional shifts are negligible and outputs the original ADP eigenvalues, anisotropy, *B*
_{eq}, *B*
_{est} and *B*
_{iso} for each atom. Analysis showed that *B*
_{est} calculated from the original anisotropic ADPs was a better predictor than *B*
_{eq} in estimating the refined value *B*
_{iso}, particularly for atoms with strong anisotropy (Fig. 2 ).

For some of the structures both *B*
_{eq} and *B*
_{est} are systematically higher than *B*
_{iso} for atoms that are almost isotropic. This effect is visible in the sample plot shown in Fig. 2(*a*) . The bias may be due to the specific choice of ADP restraint weights used either in the original *SHELXL* anisotropic refinement or in the isotropic *REFMAC* refinement. However, since *B*
_{eq} and *B*
_{est} converge as the anisotropy goes to 1, this effect has little impact on the relative accuracy of the two predictors. *B*
_{est} is more accurate overall (Table 1 ). For one structure (2b97, bottom curve in Fig. 2*b*
), *B*
_{est} is a poorer predictor of *B*
_{iso} for atoms with anisotropy near 0.5; but, even for this structure, *B*
_{est} is more accurate overall (Table 1 ).

TLS analysis was originally introduced to examine an experimentally determined set of anisotropic ADPs for evidence of chemical moieties undergoing approximately rigid-body displacement. The method has been adapted to generate models for macromolecular refinement. In this context the refined ADPs that constitute the starting point for TLS analysis are usually isotropic. The isotropic form of the *TLSMD* method introduced by Painter & Merritt (2006 ) finds an optimal N-group segmentation of a polymer chain by jointly varying the assignment of atoms to groups and the assignment of values to each group’s TLS parameters so as to minimize the residual,

Here, *B*
_{iso} for each atom is the refined isotropic ADP provided as input, and *B*
_{TLS} for that atom is the predicted isotropic displacement derived from the TLS parameters being refined for the group it belongs to. The formula used to calculate *B*
_{TLS} up to now has been = ; *i.e.* it is the *B*
_{eq} of the anisotropic ADP for that atom. In this formulation only ten independent TLS parameters, rather than the full set of 20, contribute to the diagonal elements needed to calculate *B*
_{TLS} (Sternberg *et al.*, 1979 ). The partial derivatives of the residual *R*
_{TLS} with respect to these ten parameters are linear. Optimization is thus computationally simple, but yields only a degenerate TLS description. The remaining parameters are not determined until the TLS model is later subjected to full crystallographic refinement.

It is reasonable to expect that use of a modified *B*
_{TLS} based on *B*
_{est} rather than *B*
_{eq} will yield lower residuals and a different minimum for the corresponding TLS parameter values. Furthermore, if *B*
_{TLS} is reformulated as *B*
_{est} then it becomes sensitive to ratios of the eigenvalues of . This means that in principle additional TLS terms will contribute to the residual *R*
_{TLS}. Thus reformulation will generate more complete TLS models owing to reduced degeneracy, at the cost of additional computational complexity arising from introduction of non-linear terms into the minimization. It is plausible, though not certain, that optimization using such a modified residual based on *B*
_{est} will consequently lead in some cases to different segmentation of the model into groups. The practical effect of this reformulation remains to be explored, as it will require substantial re-working of the *TLSMD* minimization code.

Because *B*
_{eq} is both well defined and easily calculated, it has been used since its introduction by W. C. Hamilton in 1959 as a convenient scalar approximation to a full anisotropic description of atomic displacement. But *B*
_{eq} is not necessarily the best value to use in all contexts where a scalar value is needed. The current paper introduces *B*
_{est} as an improved estimator for the experimentally obtained isotropic value given an initial anisotropic model for the true electron density. It seems likely that all TLS analyses of isotropic models, including the use of *TLSMD* to create segmented models of macromolecular structures, would benefit from its adoption. Finally, the demonstration that *B*
_{eq} is an overestimate for *B*
_{iso} provides an explanation for anecdotal reports that TLS refinement results in higher *B* factors.

This work was supported by NIH award R01GM080232. Source code for version 1.1 of the *coruij* program can be downloaded from http://www.bmsc.washington.edu/parvati/.

- Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C. & Zwart, P. H. (2010).
*Acta Cryst.*D**66**, 213–221. [PMC free article] [PubMed] - Berman, H., Henrick, K., Nakamura, H. & Markley, J. L. (2007).
*Nucleic Acids Res.***35**, D301–D303. [PMC free article] [PubMed] - Burnett, M. N. & Johnson, C. K. (1996).
*ORTEP-III: Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations.*Report ORNL-6895. Oak Ridge National Laboratory, TN, USA. - Chen, X., Poon, B. K., Dousis, A., Wang, Q. & Ma, J. (2007).
*Structure*,**15**, 955–962. [PMC free article] [PubMed] - Hamilton, W. C. (1959).
*Acta Cryst.***12**, 609–610. - Hinsen, K. (2008).
*Bioinformatics*,**24**, 521–528. [PubMed] - Howlin, B., Moss, D. S. & Harris, G. W. (1989).
*Acta Cryst.*A**45**, 851–861. [PubMed] - IUCr Commission on Journals (1986).
*Acta Cryst.*C**42**, 1100. - Kullback, S. & Leibler, R. A. (1951).
*Ann. Math. Stat.***22**, 79–86 (http://projecteuclid.org/euclid.aoms/1177729694). - Merritt, E. A. (1999
*a*).*Acta Cryst.*D**55**, 1997–2004. [PubMed] - Merritt, E. A. (1999
*b*).*Acta Cryst.*D**55**, 1109–1117. [PubMed] - Merritt, E. A. (2011).
*Acta Cryst.*D. In the press. - Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011).
*Acta Cryst.*D**67**, 355–367. [PMC free article] [PubMed] - Painter, J. & Merritt, E. A. (2006).
*Acta Cryst.*D**62**, 439–450. [PubMed] - Poon, B. K., Chen, X., Lu, M., Vyas, N. K., Quiocho, F. A., Wang, Q. & Ma, J. (2007).
*Proc. Natl Acad. Sci. USA*,**104**, 7869–7874. [PubMed] - Schneider, T. R. (1996). In
*Proceeding of the*, edited by E. Dodson, M. Moore, A. Ralph and S. Bailey, pp. 133–144. Warrington: Daresbury Laboratory.*CCP4*Study Weekend - Sheldrick, G. M. & Schneider, T. R. (1997).
*Methods Enzymol.***277**, 319–343. [PubMed] - Sternberg, M. J., Grace, D. E. & Phillips, D. C. (1979).
*J. Mol. Biol.***130**, 231–252. [PubMed] - Trueblood, K. N. (1978).
*Acta Cryst.*A**34**, 950–954. - Trueblood, K. N., Bürgi, H.-B., Burzlaff, H., Dunitz, J. D., Gramaccioli, C. M., Schulz, H. H., Shmueli, U. & Abrahams, S. C. (1996).
*Acta Cryst.*A**52**, 770–781. - Winn, M. D., Isupov, M. N. & Murshudov, G. N. (2001).
*Acta Cryst.*D**57**, 122–133. [PubMed] - Zucker, F., Champ, P. C. & Merritt, E. A. (2010).
*Acta Cryst.*D**66**, 889–900. [PMC free article] [PubMed]

Articles from Acta Crystallographica Section A: Foundations of Crystallography are provided here courtesy of **International Union of Crystallography**

PubMed Central Canada is a service of the Canadian Institutes of Health Research (CIHR) working in partnership with the National Research Council's national science library in cooperation with the National Center for Biotechnology Information at the U.S. National Library of Medicine(NCBI/NLM). It includes content provided to the PubMed Central International archive by participating publishers. |