Neutron and X-ray analysis of the Fenna–Matthews–Olson photosynthetic antenna complex from Prosthecochloris aestuarii

The Fenna–Matthews–Olson protein from Prosthecochloris aestuarii (PaFMO) has been crystallized in a new form that is amenable to high-resolution X-ray and neutron analysis. The crystals belonged to space group H3, with unit-cell parameters a = b = 83.64, c = 294.78 Å, and diffracted X-rays to ∼1.7 Å resolution at room temperature. Large PaFMO crystals grown to volumes of 0.3–0.5 mm3 diffracted neutrons to 2.2 Å resolution on the MaNDi neutron diffractometer at the Spallation Neutron Source. The resolution of the neutron data will allow direct determination of the positions of H atoms in the structure, which are believed to be fundamentally important in tuning the individual excitation energies of bacteriochlorophylls in this archetypal photosynthetic antenna complex. This is one of the largest unit-cell systems yet studied using neutron diffraction, and will allow the first high-resolution neutron analysis of a photosynthetic antenna complex.

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The structures of marialite (Me6) and meionite (Me93) in space groups P42/n and I4/m, and the absence of phase transitions in the scapolite series

Powder Diffraction ◽

10.1154/1.3582802 ◽

2011 ◽

Vol 26 (2) ◽

pp. 119-125 ◽

Cited By ~ 1

Author(s):

Sytle M. Antao ◽

Ishmael Hassan

Keyword(s):

Phase Transitions ◽

High Resolution ◽

Crystal Structures ◽

Unit Cell ◽

X Ray Diffraction ◽

Unit Cell Parameters ◽

X Ray ◽

Space Groups ◽

Cell Parameters ◽

The Mean

The crystal structures of marialite (Me6) from Badakhshan, Afghanistan and meionite (Me93) from Mt. Vesuvius, Italy were obtained using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and Rietveld structure refinements. Their structures were refined in space groups I4/m and P42/n, and similar results were obtained. The Me6 sample has a formula Ca0.24Na3.37K0.24[Al3.16Si8.84O24]Cl0.84(CO3)0.15, and its unit-cell parameters are a=12.047555(7), c=7.563210(6) Å, and V=1097.751(1) Å3. The average ⟨T1-O⟩ distances are 1.599(1) Å in I4/m and 1.600(2) Å in P42/n, indicating that the T1 site contains only Si atoms. In P42/n, the average distances of ⟨T2-O⟩=1.655(2) and ⟨T3-O⟩=1.664(2) Å are distinct and are not equal to each other. However, the mean ⟨T2,3-O⟩=1.659(2) Å in P42/n and is identical to the ⟨T2′-O⟩=1.659(1) Å in I4/m. The ⟨M-O⟩ [7]=2.754(1) Å (M site is coordinated to seven framework O atoms) and M-A=2.914(1) Å; these distances are identical in both space groups. The Me93 sample has a formula of Na0.29Ca3.76[Al5.54Si6.46O24]Cl0.05(SO4)0.02(CO3)0.93, and its unit-cell parameters are a=12.19882(1), c=7.576954(8) Å, and V=1127.535(2) Å3. A similar examination of the Me93 sample also shows that both space groups give similar results; however, the C–O distance is more reasonable in P42/n than in I4/m. Refining the scapolite structure near Me0 or Me100 in I4/m forces the T2 and T3 sites (both with multiplicity 8 in P42/n) to be equivalent and form the T2′ site (with multiplicity 16 in I4/m), but ⟨T2-O⟩ is not equal to ⟨T3-O⟩ in P42/n. Using different space groups for different regions across the series implies phase transitions, which do not occur in the scapolite series.

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Crystal-structure analysis of four mineral samples of anhydrite, CaSO4, using synchrotron high-resolution powder X-ray diffraction data

Powder Diffraction ◽

10.1154/1.3659285 ◽

2011 ◽

Vol 26 (4) ◽

pp. 326-330 ◽

Cited By ~ 14

Author(s):

Sytle M. Antao

Keyword(s):

Crystal Structure ◽

High Resolution ◽

Unit Cell Volume ◽

Crystal Structure Analysis ◽

Unit Cell ◽

X Ray Diffraction ◽

Unit Cell Parameters ◽

Rietveld Refinements ◽

X Ray ◽

Cell Parameters

The crystal structures of four samples of anhydrite, CaSO4, were obtained by Rietveld refinements using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and space group Amma. As an example, for one sample of anhydrite from Hants County, Nova Scotia, the unit-cell parameters are a = 7.00032(2), b = 6.99234(1), c = 6.24097(1) Å, and V = 305.487(1) Å3 with a > b. The eight-coordinated Ca atom has an average <Ca-O> distance of 2.4667(4) Å. The tetrahedral SO4 group has two independent S-O distances of 1.484(1) to O1 and 1.478(1) Å to O2 and an average <S-O> distance of 1.4810(5) Å. The three independent O-S-O angles [108.99(8) × 1, 110.38(3) × 4, 106.34(9)° × 1; average <O-S-O> [6] = 109.47(2)°] and S-O distances indicate that the geometry of the SO4 group is quite distorted in anhydrite. The four anhydrite samples have structural trends where the a, b, and c unit-cell parameters increase linearly with increasing unit-cell volume, V, and their average <Ca-O> and <S-O> distances are nearly constant. The grand mean <Ca-O> = 2.4660(2) Å, and grand mean <S-O> = 1.4848(3) Å, the latter is longer than 1.480(1) Å in celestite, SrSO4, as expected.

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Ultra-stable sub-meV monochromator for hard X-rays

Journal of Synchrotron Radiation ◽

10.1107/s1600577515012230 ◽

2015 ◽

Vol 22 (5) ◽

pp. 1155-1162 ◽

Cited By ~ 1

Author(s):

T. S. Toellner ◽

J. Collins ◽

K. Goetze ◽

M. Y. Hu ◽

C. Preissner ◽

...

Keyword(s):

High Resolution ◽

Synchrotron Radiation ◽

High Speed ◽

Room Temperature ◽

Energy Calibration ◽

Nuclear Transition ◽

X Rays ◽

Excitation Energies ◽

Transmitted Beam ◽

X Ray

A high-resolution silicon monochromator suitable for 21.541 keV synchrotron radiation is presented that produces a bandwidth of 0.27 meV. The operating energy corresponds to a nuclear transition in151Eu. The first-of-its-kind, fully cryogenic design achieves an energy-alignment stability of 0.017 meV r.m.s. per day, or a 100-fold improvement over other meV-monochromators, and can tolerate higher X-ray power loads than room-temperature designs of comparable resolution. This offers the potential for significantly more accurate measurements of lattice excitation energies using nuclear resonant vibrational spectroscopy if combined with accurate energy calibration using, for example, high-speed Doppler shifting. The design of the monochromator along with its performance and impact on transmitted beam properties are presented.

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Structure of β-trimyristin and β-tristearin from high-resolution X-ray powder diffraction data

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768100019121 ◽

2001 ◽

Vol 57 (3) ◽

pp. 372-377 ◽

Cited By ~ 26

Author(s):

Arjen van Langevelde ◽

René Peschar ◽

Henk Schenk

Keyword(s):

High Resolution ◽

Powder Diffraction ◽

Diffraction Data ◽

Unit Cell ◽

Grid Search ◽

Powder Diffraction Data ◽

Unit Cell Parameters ◽

X Ray ◽

Cell Parameters ◽

Distance Restraints

The crystal structures of β-1,2,3-tritetradecanoylglycerol (β-trimyristin or β-MMM) and β-1,2,3-trioctadecanoylglycerol (β-tristearin or β-SSS) have been determined from high-resolution synchrotron X-ray powder diffraction data. Grid search and Rietveld refinement have been used to determine and refine the structure, respectively. Both substances crystallize in space group P\bar 1 with Z = 2. The unit-cell parameters for β-MMM are a = 12.0626 (6), b = 41.714 (1), c = 5.4588 (3) Å, α = 73.388 (4), β = 100.408 (5) and γ = 118.274 (4)°. For β-SSS the unit-cell parameters are a = 12.0053 (7), b = 51.902 (2), c = 5.4450 (3) Å, α = 73.752 (5), β = 100.256 (6) and γ = 117.691 (5)°. Soft-distance restraints have been applied to the molecules during refinement. For β-MMM the final Rp value obtained is 0.053 and for β-SSS the final Rp value is 0.041.

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Crystallization and preliminary X-ray analysis of a complex between the Bowman–Birk trypsin inhibitor from barley and porcine pancreatic trypsin

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444999005065 ◽

1999 ◽

Vol 55 (6) ◽

pp. 1244-1246 ◽

Cited By ~ 1

Author(s):

Young Sil Kim ◽

Hyun Kyu Song ◽

Se Won Suh

Keyword(s):

Polyethylene Glycol ◽

Trypsin Inhibitor ◽

Unit Cell ◽

X Rays ◽

Asymmetric Unit ◽

Unit Cell Parameters ◽

Orthorhombic Space Group ◽

Solvent Content ◽

X Ray ◽

Cell Parameters

A 1:2 complex between the Bowman–Birk trypsin inhibitor from barley seeds and porcine pancreatic trypsin has been crystallized at 291 K using polyethylene glycol as precipitant. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 67.10, b = 88.38 and c = 203.65 Å. The asymmetric unit contains two monomers of the complex, with a corresponding Vm of 2.41 Å3 Da−1 and a solvent content of 49%. Native data to 2.2 Å resolution have been collected at 100 K using synchrotron X-rays.

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The crystal structure of tin sulphate, SnSO4, and comparison with isostructural SrSO4, PbSO4, and BaSO4

Powder Diffraction ◽

10.1017/s0885715612000450 ◽

2012 ◽

Vol 27 (3) ◽

pp. 179-183 ◽

Cited By ~ 2

Author(s):

Sytle M. Antao

Keyword(s):

Crystal Structure ◽

High Resolution ◽

Rietveld Refinement ◽

Structural Parameters ◽

Lone Pair ◽

Unit Cell ◽

X Ray Diffraction ◽

Unit Cell Parameters ◽

X Ray ◽

Cell Parameters

The crystal structure of tin (II) sulphate, SnSO4, was obtained by Rietveld refinement using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data. The structure was refined in space group Pbnm. The unit-cell parameters for SnSO4 are a = 7.12322(1), b = 8.81041(1), c = 5.32809(1) Å, and V = 334.383(1) Å3. The average 〈Sn–O〉 [12] distance is 2.9391(4) Å. However, the Sn2+cation has a pyramidal [3]-coordination to O atoms and the average 〈Sn–O〉 [3] = 2.271(1) Å. If Sn is considered as [12]-coordinated, SnSO4 has a structure similar to barite, BaSO4, and its structural parameters are intermediate between those of BaSO4 and PbSO4. The tetrahedral SO4 group has an average 〈S–O〉 [4] = 1.472(1) Å in SnSO4. Comparing SnSO4 with the isostructural SrSO4, PbSO4, and BaSO4, several well-defined trends are observed. The radii, rM, of the M2+(=Sr, Pb, Sn, and Ba) cations and average 〈S–O〉 distances vary linearly with V because of the effective size of the M2+cation. Based on the trend for the isostructural sulphates, the average 〈Sn–O〉 [12] distance is slightly longer than expected because of the lone pair of electrons on the Sn2+cation.

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Crystallization and preliminary X-ray analyses of catabolite control protein A, free and in complex with its DNA-binding site

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444999013104 ◽

2000 ◽

Vol 56 (1) ◽

pp. 67-69 ◽

Cited By ~ 1

Author(s):

Jan Tebbe ◽

Peter Orth ◽

Elke Küster-Schöck ◽

Wolfgang Hillen ◽

Wolfram Saenger ◽

...

Keyword(s):

Protein A ◽

Unit Cell ◽

X Rays ◽

Asymmetric Unit ◽

Unit Cell Parameters ◽

Space Group ◽

X Ray ◽

Cell Parameters ◽

Control Protein ◽

Catabolite Control

The catabolite control protein (CcpA) from Bacillus megaterium is a member of the bacterial repressor protein family GalR/LacI. CcpA with an N-terminal His-tag was used for crystallization. Crystals of free CcpA and of CcpA in complex with the putative operator sequence (catabolite responsive elements, CRE) were obtained by vapour-diffusion techniques at 291 K using the hanging-drop method. CcpA crystals grown in the presence of polyethylene glycol 8000 belong to the hexagonal space group P6122 or P6522, with unit-cell parameters a = 74.4, c = 238.8 Å. These crystals diffract X-rays to 2.55 Å resolution and contain one monomer of the homodimeric protein per asymmetric unit. Crystals of the CcpA–CRE complex were obtained with ammonium sulfate as precipitant and belong to the tetragonal space group I4122, with unit-cell parameters a = 125, c = 400 Å and one complex per asymmetric unit. Although these co-crystals grew to a sufficient size, X-ray diffraction was limited to 8 Å resolution.

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Energy-dispersive Laue diffraction by means of a pnCCD detector coupled to a CsI(Tl) scintillator using ultra-hard X-ray synchrotron radiation

Journal of Synchrotron Radiation ◽

10.1107/s160057751900626x ◽

2019 ◽

Vol 26 (5) ◽

pp. 1612-1620

Author(s):

Mohammad Shokr ◽

Amir Tosson ◽

Ali Abboud ◽

Alaa Algashi ◽

Dieter Schlosser ◽

...

Keyword(s):

Detection System ◽

Unit Cell ◽

Lattice Parameters ◽

Energy Dispersive ◽

Mean Deviation ◽

X Rays ◽

Laue Diffraction ◽

High Quantum Efficiency ◽

X Ray ◽

Cell Parameters

The lattice parameters and unit-cell orientation of an SrLaAlO4 crystal have been determined by means of energy-dispersive X-ray Laue diffraction (EDLD) using a pnCCD detector coupled to a columnar structure CsI(Tl) scintillator in the energy range between 40 and 130 keV. By exploiting the high quantum efficiency (QE) achieved by this combined detection system for hard X-rays, a large number of Bragg reflections could be recorded by the relatively small detector area, allowing accurate and fast determination of the lattice parameters and the moduli of the structure factors. The experiment was performed on the energy-dispersive diffraction (EDDI) beamline at the BESSY II synchrotron using a pnCCD detector with 128 × 128 pixels. Since the energies and positions of the Laue peaks can be recorded simultaneously by the pnCCD system, the tetragonal structure of the investigated specimen was determined without any prior information. The unit-cell parameters and the angles between the lattice vectors were evaluated with an accuracy of better than 0.7%, while the structure-factor moduli of the reflections were determined with a mean deviation of 2.5% relative to the theoretical values.

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Structure of C n C n+2C n -type (n = even) β′-triacylglycerols

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768100009927 ◽

2000 ◽

Vol 56 (6) ◽

pp. 1103-1111 ◽

Cited By ~ 45

Author(s):

Arjen Van Langevelde ◽

Kees Van Malssen ◽

René Driessen ◽

Kees Goubitz ◽

Frank Hollander ◽

...

Keyword(s):

High Resolution ◽

Crystal Structures ◽

Powder Diffraction ◽

Chair Conformation ◽

Unit Cell ◽

Unit Cell Parameters ◽

X Ray ◽

Cell Parameters ◽

Β Phase ◽

Acyl Chains

The crystal structures of the β′ phase of CLC (1,3-didecanoyl-2-dodecanoylglycerol) and MPM (1,3-ditetradecanoyl-2-hexadecanoylglycerol) have been determined from single-crystal X-ray diffraction and high-resolution X-ray powder diffraction data, respectively. Both these crystals are orthorhombic with space group Iba2 and Z = 8. The unit-cell parameters of β′-CLC are a = 57.368 (6), b = 22.783 (2) and c = 5.6945 (6) Å and the final R value is 0.175. The unit-cell parameters of β′-MPM are a = 76.21 (4), b = 22.63 (1) and c = 5.673 (2) Å and the final Rp value is 0.057. Both the β′-CLC and β′-MPM molecules are crystallized in a chair conformation, having a bend at the glycerol moiety. The zigzag planes of the acyl chains are orthogonally packed, as is typical for a β′ phase. Furthermore, unit-cell parameters of some other members of the C n C n+2C n -type triacylglycerol series have been refined on their high-resolution X-ray powder diffraction pattern. Finally, the crystal structures are compared with the currently known structures and models of triacylglycerols.

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Crystal Structure Refinements of Four Monazite Samples from Different Localities

Minerals ◽

10.3390/min10111028 ◽

2020 ◽

Vol 10 (11) ◽

pp. 1028 ◽

Cited By ~ 1

Author(s):

M. Mashrur Zaman ◽

Sytle M. Antao

Keyword(s):

Crystal Structure ◽

Electron Probe ◽

Unit Cell Volume ◽

Unit Cell ◽

X Ray Diffraction ◽

Unit Cell Parameters ◽

X Ray ◽

Cell Parameters ◽

Large Unit Cell ◽

A Site

This study investigates the crystal chemistry of monazite (APO4, where A = Lanthanides = Ln, as well as Y, Th, U, Ca, and Pb) based on four samples from different localities using single-crystal X-ray diffraction and electron-probe microanalysis. The crystal structure of all four samples are well refined, as indicated by their refinement statistics. Relatively large unit-cell parameters (a = 6.7640(5), b = 6.9850(4), c = 6.4500(3) Å, β = 103.584(2)°, and V = 296.22(3) Å3) are obtained for a detrital monazite-Ce from Cox’s Bazar, Bangladesh. Sm-rich monazite from Gunnison County, Colorado, USA, has smaller unit-cell parameters (a = 6.7010(4), b = 6.9080(4), c = 6.4300(4) Å, β = 103.817(3)°, and V = 289.04(3) Å3). The a, b, and c unit-cell parameters vary linearly with the unit-cell volume, V. The change in the a parameter is large (0.2 Å) and is related to the type of cations occupying the A site. The average <A-O> distances vary linearly with V, whereas the average <P-O> distances are nearly constant because the PO4 group is a rigid tetrahedron.

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