F. J. Rotella

The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results

The 19ID undulator beamline of the Structure Biology Center has been designed and built to take full advantage of the high flux, brilliance and quality of X-ray beams delivered by the Advanced Photon Source. The beamline optics are capable of delivering monochromatic X-rays with photon energies from 3.5 to 20 keV (3.5-0.6 A wavelength) with fluxes up to 8-18 x 10(12) photons s(-1) (depending on photon energy) onto cryogenically cooled crystal samples. The size of the beam (full width at half-maximum) at the sample position can be varied from 2.2 mm x 1.0 mm (horizontal x vertical, unfocused) to 0.083 mm x 0.020 mm in its fully focused configuration. Specimen-to-detector distances of between 100 mm and 1500 mm can be used. The high flexibility, inherent in the design of the optics, coupled with a kappa-geometry goniometer and beamline control software allows optimal strategies to be adopted in protein crystallographic experiments, thus maximizing the chances of their success. A large-area mosaic 3 x 3 CCD detector allows high-quality diffraction data to be measured rapidly to the crystal diffraction limits. The beamline layout and the X-ray optical and endstation components are described in detail, and the results of representative crystallographic experiments are presented.

Crystal structure and thermal expansion of α‐quartz SiO2 at low temperatures

The crystal structure of α‐SiO2 (low quartz) has been refined at 296, 78, and 13 K from time‐of‐flight neutron powder diffraction data. The major effect of temperature from 296 to 78 K is a nearly rigid body rotation of the SiO4 tetrahedra. Below 78 K, tetrahedral rotation is substantially reduced giving rise to a much smaller thermal expansion. A comparison of the volume dependence of the Si‐O‐Si angle, the rotation angle for SiO4 tetrahedra and the c/a ratio suggests that the mechanism for expansion may be changing from tetrahedral rotation to tetrahedral distortion at the lowest temperatures. The inverse linear relation between the mean Si‐O bond distance and −sec(Si‐O‐Si) which has been observed for silica minerals at both ambient and high‐temperature conditions appears to be consistent with the structural variations that occur at low temperatures.

Crystal structure and thermal expansion of. cap alpha. -quartz SiO/sub 2/ at low temperatures

The crystal structure of α‐SiO2 (low quartz) has been refined at 296, 78, and 13 K from time‐of‐flight neutron powder diffraction data. The major effect of temperature from 296 to 78 K is a nearly rigid body rotation of the SiO4 tetrahedra. Below 78 K, tetrahedral rotation is substantially reduced giving rise to a much smaller thermal expansion. A comparison of the volume dependence of the Si‐O‐Si angle, the rotation angle for SiO4 tetrahedra and the c/a ratio suggests that the mechanism for expansion may be changing from tetrahedral rotation to tetrahedral distortion at the lowest temperatures. The inverse linear relation between the mean Si‐O bond distance and −sec(Si‐O‐Si) which has been observed for silica minerals at both ambient and high‐temperature conditions appears to be consistent with the structural variations that occur at low temperatures.

Neutron diffraction and ion-channeling investigations of atomic displacements in YBa2Cu3O7-δ between 10 and 300 K

Abstract Neutron powder diffraction was used to investigate the structural and vibrational properties of a single-phase ceramic specimen of YBa 2 Cu 3 O 7-δ in the temperature range from 10 to 300 K. Measurements were taken at closely-spaced (10 K) intervals between 50 and 150 K, and the data were defined to a precision equal to or exceeding that achieved in previous studies. No clear evidence is found for an anomalous change in any of the structural parameters, including the orthorhombicity parameter, 2( b - a )/( a + b ), in the vicinity of T c . The vibrational properties obtained from the neutron diffraction data are compared with previous results from ion-channeling in single-crystals of YBa 2 Cu 3 O 7-δ , these latter results revealed a clear anomaly at T c in displacements of the Cu(1), Cu(2) and O(4) atoms in the a - b plane. The average vibrational properties of the lattice atoms determined from the two techniques agree quite well, showing an overall decrease in the apparent vibrational amplitude from 300 to 100 K, followed by a further drop as the temperature is lowered through T c . The evidence for an abrupt change (≈0.015 A) in displacement amplitude at T c is clearly much stronger in the channeling results; the magnitude of any anomaly in the diffraction results approaches the statistical uncertainty. The absence of a clear abrupt change in the neutron results at T c suggests that the ion channeling anomaly is not due to an overall reduction in average vibration, amplitude, but arises instead from a strongly correlated sequence of Cu and O (4) displacements appearing in the superconducting state.

Thermal expansion measurements using neutron diffraction of Bi2CaSr2Cu2Ox

Abstract The differential thermal expansion of Bi 2 CaSr 2 Cu 2 O x , Bi-(2122), has been measured using high-temperature neutron powder diffraction in air, 0.980% oxygen in nitrogen, and pure argon. Thermal expansion in the c -axis direction is greater by a factor of about 1.4 than that in either the a - or b -axis direction for all sample environments. The neutron results for Bi-(2122) in air are compared with results from similar X-ray powder diffraction measurements.

Neutron powder diffraction study of defect spinel structures: Tetrahedrally coordinated Ti4+ in Ni2.62Ti0.69O4 and Ni2.42Ti0.74Si0.05O4

Cation-excess spinels with the general formula Ni2(1 + x)2 +(Si4+, Ti4+)(1 − x)O4 (0.16 ≤ x ≤ 1) can be considered as defect NiO rocksalt structures in which two octahedral metal atoms are replaced by one tetrahedrally coordinated atom. Neutron time-of-flight powder data have been collected for two members of the solid-solution series with the ZING-P′ high-resolution diffractometer at Argonne National Laboratory. Least-squares refinement, using a modified Rietveld profile analysis, confirms that all Ti4+ in Ni2.62Ti0.69O4 [R(profile) = 3.27%; R(Rietveld) = 9.06%] and Ni2.42Ti0.74Si0.05O4 [R(profile) = 3.07%; R(Rietveld) = 8.54%] partially occupies the tetrahedral site 8(a) (Fd3m). Ni2+ totally occupies the octahedral position 16(d) and partially occupies position 16(c) which is vacant in stoichiometric spinels. The presence of small amounts of Si4+ (~ 3 mol%) in the tetrahedral site 8(a) stabilizes the structure and results in a large decrease [0.0194 (1) A] in the a cell parameter.

Neutron powder diffraction of forsterite, Mg2SiO4: a comparison with single-crystal investigations

Neutron time-of-flight powder data have been collected for forsterite [Mg2SiO4; Pbnm (D162h, No. 62); Z = 4, a = 4.7534 (1), b = 10.1989 (2), c = 5.9813 (1) A] with the ZING-P′ high-resolution diffractometer at Argonne National Laboratory. Forty-seven variables, including anisotropic temperature-factor coefficients, were refined with a profile-fitting procedure to R(profile) = 2.10% and R(Rietveld) = 3.53%. Positional and thermal parameters are in good agreement with those determined from recent X-ray and neutron single-crystal diffraction experiments. Results suggest that powder data can be used to obtain accurate positional parameters and reasonable temperature factors for moderately complex structures.

Is your cold-stream working for you or against you? An in-depth look at temperature and sample motion

It is normally assumed that a commercial gaseous nitrogen cold-stream provides a sample environment near 100 K and that the force of the cold-stream does not induce movement in the sample. As might be expected, the reality is much more complex. Here, an investigation of one cold-stream, starting with the temperature profile, is presented. Using silicon single crystals and flexible mounting loops, an approximate force/vibration profile of the cold-stream is obtained. Results indicate that the center of the temperature profile is offset from the position suggested by the manufacturer-supplied alignment tool and coincides with the area within the cold-stream that has the most consistent force profile. Tests indicate that this region is only about one-third of the width of the cold-stream nozzle opening. To verify that the results were relevant to protein crystallographic data collection, the impact of cold-stream position on the final data quality for lysozyme crystals was analyzed. On the basis of the observations it is recommended that users perform a temperature profile of their cold-streams to ensure proper alignment instead of relying only on the alignment tool for setup. In addition, suggestions are made on what users can look for in data processing to identify problems with loop movement and what users can do to minimize the impact of these problems on their experiments.

Electrical properties and crystal structures of the homologous series of oxides Nd2Ba2CamCenTi2−δCu2+δO11+m+2n (m, n = 0 or 1)

Abstract Four oxides belonging to the homologous series with the general formula Nd 2 Ba 2 Ca m Ce n Ti 2−δ Cu 2+δ O 11+ m +2 n , were prepared for m , n = 0 or 1. Although all of these oxides have two-dimensional CuO 2 planes, they do not show any superconductivity, only a normal paramagnetic behavior. Their crystal structures were analyzed by TOF neutron powder diffraction. Nd 2 Ba 2 Ti 1.908 Cu 2.092 O 11 ( m =0, n =0 and δ =0.09) is isomorphous with Gd 2 Ba 2 Ti 2 Cu 2 O 11 . The structures of the other three oxides can be derived from that of Nd 2 Ba 2 Ti 1.908 Cu 2.092 O 11 . The structure of Nd 2 Ba 2 Ti 1.92 Cu 2.08 O 12 ( m =1, n =0 and δ =0.08) is obtained by the substitution of rock-salt-type (Ca,Nd,Ba)O(Ca,Nd,Ba)O layers for the (Nd,Ba)O layer. The structure of Nd 2 Ba 2 CeTi 2 Cu 2 O 13 ( m =0, n =1 and δ =0) is characterized by the insertion of fluorite-type (Nd,Ce)O 2 (Nd,Ce) layers in the place of the Nd layer. Nd 2 Ba 2 CaCeTi 2 Cu 2 O 14 ( m =1, n =1, and δ =0) results from the alternate substitutions of rock-salt-type and fluorite-type layers for the (Nd,Ba)O and Nd layers, respectively.

Re-thinking the role of the beamstop at a synchrotron-based protein crystallography beamline

A 1 mm vertical-profile X-ray beamstop has been designed to operate in the energy range 6-20 keV. The relationship between the beamstop-to-sample distance and air scatter is discussed with the intent of establishing criteria for optimal beamstop positioning during an experiment. Different choices for beamstop materials are described with respect to stopping power, fluorescence and scattering from the surface. Suggestions for improvements in beamstop design are presented which are applicable for future automation and equipment safety. All work was performed on the Structural Biology Center insertion-device beamline, 19ID, at the Advanced Photon Source.