Structure Determination and Refinement

Structure Determination and Refinement. Intensity data are usually recorded at two or more nozzle-to-plate distances. A composite experimental intensity curve is then constructed and used to compute an experimental RD curve according to equation (39). This RD curve combined with the knowledge of reasonable values for some of the structural parameters, gives in many cases an initial model accurate enough to start a least-squares refinement. In other cases it is advantageous to calculate a number of theoretical curves 

The structural parameters (r, u, sometimes k, and possibly other parameters) are then obtained by least-squares fitting, usually on the intensity curves, but occasionally on the RD curves (c/. p. 45). If the intensity data are used, the data from all the nozzle-to-plate distances are not necessarily combined into one composite curve an individual scale factor may be refined for each set of data. Since the observed data are considerably correlated, i.e. each point cannot be regarded as an independent observation, a number of problems are encountered in the application of the least-squares method. This problem is most important for the estimation of the standard deviations, since the parameters may be obtained fairly satis-factorally by conventional least-squares refinement. (A more detailed discussion is set out on p. 45.) 

It is in most cases not possible to refine all interatomic distances and u values as independent parameters. Based on an assumed molecular model, dependent distances may be calculated from independent distance and angle parameters. However, as mentioned above, and r structures are not geometrically consistent. One may therefore either use r,j structures or correct for the shrinkage effects. If the harmonic force field is not known, the shrinkage is often neglected. This introduces significant, but usually fairly small, errors in the structural parameters cf. Table 8). 

Hamilton, Statistics in Physical Science , The Ronald Press Co., New York, 1964. 

The double peak is perhaps better understood if the intensity contributions from two nearly equal distances (rt and r ) of the same type and with the same value is considered. In the simplest approximation 

---

Matias, P. M., Soares, C. M., Saraiva, L. M., Coelho, R., Morais, J., LeGall, J. and Carrondo, M. A. (2001) [NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774 gene sequencing, three-dimensional structure determination and refinement at 1.8 angstrom and... 

Once a structure determination and refinement have been carried out, several tests are available for deciding whether the chosen absolute structure or its inverse is correct. The most important tests are discussed in their historical order. 

Diversity analysis and physical property calculation were performed by Ceris2 (4). HKL package was applied for X-ray data process (6) and the X-ray structure determination and refinement were carried out by CNX (4). X-ray co-crystal complex structures discussed in this chapter were deposited in PDB database with codes 205D, 2HWH, 2HWI, and 21 IK... 

Crystals and X-ray Data Collection. Detailed information concerning protein purification, crystallization, and X-ray data collection can be found in a previous report (Xu et al., 1991) and will be mentioned here in summary form. Recombinant murine apo-ALBP crystallizes in the orthorhombic space group P2j2i2i with the following unit cell dimensions a = 34.4 A, b = 54.8 A, and c = 76.3 A. The asymmetric unit contains one molecule with a molecular weight of 14,500. The entire diffraction data set was collected on one crystal. In the resolution range t -2.5 A, 5115 of the 5227 theoretically possible reflections were measured. Unless otherwise noted the diffraction data with intensities greater than 2a were used for structure determination and refinement. As can be seen in Table 8.2, this included about 96% of the measured data. 

Table I. Crystal Data and Details of the Structure Determination and Refinement for XeF5 AgF4"...

Thus, a fast experiment is routinely suitable for evaluation of the specimen and phase identification, i.e. qualitative analysis. When needed, it should be followed by a weekend experiment for a complete structural determination. An overnight experiment is required for indexing and accurate lattice parameters refinement, and a weekend-long experiment is needed for crystal structure determination and refinement. In some instances, e.g. when a specimen has exceptional quality and its crystal structure is known or very simple, all relevant parameters can be determined using data collected in an overnight experiment. Similarly, fast experiment(s) may be suitable for unit cell determination in addition to phase identification. In any case, one should use his/her own judgment and experience to assess both the suitability of the experimental data and the reliability of the result. 

Sir2004/CAOS S1R2004 an improved tool for crystal structure determination and refinement, M. C. Sir2004 CAOS... 

C. Giacovazzo, A. Guagliardi, A. G. G. Moliterni, G. Polidori and R. Spagna, J. Appl. Crystallogr., 1999, 32, 115 119 and SIR2004 an improved tool for crystal structure determination and refinement, M. C. Burla,... 

UppENBERG, J., Hansen, M.T., Patkar, S. and Jones, T.A. (1994) Sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica. Structure 2, 293-308... 

Crystal Structure Determination and Refinement of 2a. The data crystal used for X-ray investigation was as small as 0.03 x 0.07 x 0.42 mm. Data were collected at -110(l) C with an Enraf-Nonius CAD4 automatic counter diffractometer controlled by a Micro VAX II computer and fitted with a low-temperature apparatus. Ni-filtered CuKa (CuKa, X = 1.54178 A, l = 14.04 cm-i) was used. Fifty reflections with 33 >0>15 and CuKai wavelength (X = 1.54051 A) were used for lattice constants. A total of 4300 reflections with 1.0 < 20 <... 

The simple model implies an infinite perfect crystal. The crystal specimen studied is necessarily finite (rarely more than 0.5 mm in size) and, if perfect by conventional criteria, would be utterly unsuitable for collection of intensity data of the kind required for ordinary structure determination and refinement. What is needed is an ideally imperfect crystal shot through with dislocations and intergrain boundaries so that it behaves, so far as diffraction is concerned, like a mosaic of perfect crystal blocks of the order of micrometers or tenths of micrometers in size, tilted with respect to one another by angles of the order of a few seconds of arc and scattering independently (incoherently) with respect to one another. The assumption of an ideally imperfect ... 

Loris, R., Steyaert, J., Maes, D., Lisgarten, J., Pickersgill, R. and Wyns, L. 1993, Crystal structure determination and refinement at 2.3-A resolution of the lentil lectin. Biochemistry 32,8772-8781. 

Cowan, S W, Newcomer, M. E., and Jones, T A (1993) Crystallographic studies on a family of cellular lipophilic transport proteins the refinement of P2 myelin protein and the structure determination and refinement of cellular retinol-bmding protein in complex with Y-trans retinol J. Mol. Biol. 230,1225-1246... 

MSe2 crystals are very brittle and have a flat, layered, tabular appearance with shiny luster. A complete structure determination and refinement have been carried out on ErSe2 single crystals (see p. 314), Wang [6], Wang, Steinfink [5]. Line diagrams of LaSe 2 SmSe 2 given in Markovskii et al. [14]. 

Line intensity Phase abundance Chemical reaction kinetics Crystal-structure determination and refinement (whole pattern) Search/match (d-l) Space-group determination (20g-absent W Preferred orientation... 

---