Crystal structure determination and refinementviaSIR2014

2015 ◽  
Vol 48 (1) ◽  
pp. 306-309 ◽  
Author(s):  
Maria Cristina Burla ◽  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Corrado Cuocci ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ab Initio ◽  
Structure Refinement ◽  
Three Dimensional ◽  
Direct Methods ◽  
Molecular Replacement ◽  
Dimensional Electron ◽  
Large Structures ◽  
Density Maps ◽  
Structure Solution

SIR2014is the latest program of theSIRsuite for crystal structure solution of small, medium and large structures. A variety of phasing algorithms have been implemented, bothab initio(standard or modern direct methods, Patterson techniques,Vive la Différence) and non-ab initio(simulated annealing, molecular replacement). The program contains tools for crystal structure refinement and for the study of three-dimensional electron-density mapsviasuitable viewers.

The revenge of the Patterson methods. II. Substructure applications

2007 ◽  
Vol 40 (2) ◽  
pp. 211-217 ◽  
Author(s):  
Maria Cristina Burla ◽  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Liberato De Caro ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ab Initio ◽  
Electron Density ◽  
Direct Methods ◽  
Large Set ◽  
Common Belief ◽  
Anomalous Diffraction ◽  
Density Maps ◽  
Structure Solution ◽  
The Common

The Patterson techniques, recently developed by the same authors for theab initiocrystal structure solution of proteins, have been applied to single and multiple anomalous diffraction (SAD and MAD) data to find the substructure of the anomalous scatterers. An automatic procedure has been applied to a large set of test structures, some of which were originally solved with remarkable difficulty. In all cases, the procedure automatically leads to interpretable electron density maps. Patterson techniques have been compared with direct methods; the former seem to be more efficient than the latter, so confirming the results obtained forab initiophasing, and disproving the common belief that they could only be applied to determine large equal-atom substructures with difficulty.

Crystallization and structure solution of p53 (residues 326–356) by molecular replacement using an NMR model as template

1998 ◽  
Vol 54 (1) ◽  
pp. 86-89 ◽  
Author(s):  
Peer R. E. Mittl ◽  
Patrick Chène ◽  
Markus G. Grütter
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Molecular Replacement ◽  
Additional Information ◽  
Nmr Structures ◽  
Replacement Method ◽  
Tetramerization Domain ◽  
Structure Solution ◽  
Molecular Replacement Method

The molecular replacement method is a powerful technique for crystal structure solution but the use of NMR structures as templates often causes problems. In this work the NMR structure of the p53 tetramerization domain has been used to solve the crystal structure by molecular replacement. Since the rotation- and translation-functions were not sufficiently clear, additional information about the symmetry of the crystal and the protein complex was used to identify correct solutions. The three-dimensional structure of residues 326–356 was subsequently refined to a final R factor of 19.1% at 1.5 Å resolution.

scholarly journals UsingFOCUSto solve zeolite structures from three-dimensional electron diffraction data

2013 ◽  
Vol 46 (4) ◽  
pp. 1017-1023 ◽  
Author(s):  
Stef Smeets ◽  
Lynne B. McCusker ◽  
Christian Baerlocher ◽  
Enrico Mugnaioli ◽  
Ute Kolb
Keyword(s):  
Electron Diffraction ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Direct Methods ◽  
Electron Diffraction Data ◽  
Chemical Information ◽  
Data Sets ◽  
Dimensional Electron ◽  
Specific Chemical ◽  
Structure Solution

The programFOCUS[Grosse-Kunstleve, McCusker & Baerlocher (1997).J. Appl. Cryst.30, 985–995] was originally developed to solve zeolite structures from X-ray powder diffraction data. It uses zeolite-specific chemical information (three-dimensional 4-connected framework structure with known bond distances and angles) to supplement the diffraction data. In this way, it is possible to compensate, at least in part, for the ambiguity of the reflection intensities resulting from reflection overlap, and the program has proven to be quite successful. Recently, advances in electron microscopy have led to the development of automated diffraction tomography (ADT) and rotation electron diffraction (RED) techniques for collecting three-dimensional electron diffraction data on very small crystallites. Reasoning that such data are also less than ideal (dynamical scattering, low completeness, beam damage) and that this can lead to failure of structure solution by conventional direct methods for very complex zeolite frameworks,FOCUSwas modified to accommodate electron diffraction data. The modified program was applied successfully to five different data sets (four ADT and one RED) collected on zeolites of different complexities. One of these could not be solved completely by direct methods but emerged easily in theFOCUStrials.

Crystal structure of a novel synthetic compound, Pb2O(OH)I, and structure refinement of ‘iodolaurionite’, Pb(OH)I: hydroxo- and oxocentred units in Pb minerals and synthetic compounds

2013 ◽  
Vol 77 (8) ◽  
pp. 3239-3248 ◽  
Author(s):  
O. I. Siidra ◽  
D. Yu. Zenko ◽  
A. N. Suknotova ◽  
S. V. Krivovichev
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Structure Refinement ◽  
Three Dimensional ◽  
Direct Methods ◽  
Hydroxyl Groups ◽  
Synthetic Compound ◽  
Synthetic Compounds ◽  
Hydrothermal Reactions

AbstractYellow needles of 'iodolaurionite', Pb(OH)I, and a novel compound Pb2O(OH)I, have been prepared by hydrothermal reactions of PbO and PbI2 at 170°C. The crystal structure of 'iodolaurionite', Pb(OH)I (orthorhombic, Pnma, a = 7.8244(8), b = 4.2107(4), c = 10.4724(10) Å, V = 345.03(6) Å3, Z = 4) has been refined to R1 = 0.041 for 129 independent observed reflections. The structure is based on the OHPb3 triangles sharing common edges to produce single [OHPb]+ chains extending along the b axis and parallel to the ab plane. The three-dimensional integrity of the structure is provided by the Pb–I bonds and the O–H···I hydrogen bonding. The structure is isotypic with that of laurionite, Pb(OH)Cl. The crystal structure of Pb2O(OH)I (monoclinic, C2/m, a = 13.711(3), b = 4.0975(10), c = 9.584(2) Å, β = 110.64(1)°, V = 503.9(2) Å3, Z = 4), has been solved by direct methods and refined to R1 = 0.053 for 586 independent observed reflections. In the structure of Pb2O(OH)I, O(1)Pb4 tetrahedra link together by sharing edges and corners to form [OPb2]2+ chains similar to those observed in sidpietersite. The O(2) atoms belong to hydroxyl groups attached to both sides of the chains to produce novel [O(OH)Pb2]+ 1D units. The [O(OH)Pb2]+ units are extended parallel to the b axis and lie within the bc plane. The [O(OH)Pb2]+ units are linked together via hydrogen bonding in the (100) plane and by weak Pb–I bonds in the [100] direction. The [O(OH)Pb2]+ bands can be obtained from the [OPb] layer of OPb4 tetrahedra present in the structure of tetragonal PbO (litharge). The continuous [OPb] layer has to be broken into [O2Pb2] bands containing 3- and 4-coordinated O atoms in the 1:1 ratio with subsequent protonation of the 3-coordinated O sites. Relations of Pb(OH)I and Pb2O(OH)I to known Pb hydroxy- and oxyhalides are described briefly.

EXPO2011: A new package for powder crystallography

2011 ◽  
Vol 26 (S1) ◽  
pp. S2-S12 ◽  
Author(s):  
Angela Altomare ◽  
Corrado Cuocci ◽  
Carmelo Giacovazzo ◽  
Anna Moliterni ◽  
Rosanna Rizzi
Keyword(s):  
Ab Initio ◽  
Simulated Annealing Algorithm ◽  
Rietveld Method ◽  
Structure Refinement ◽  
A Priori ◽  
Direct Methods ◽  
Molecular Geometry ◽  
Real Space ◽  
Basic Algorithm ◽  
Structure Solution

EXPO2011 is a new package for phasing crystal structures from powder diffraction diagrams. It is able to carry out all the steps necessary for crystal structure solution, from pattern indexation up to Rietveld method for structure refinement: for each step, the basic algorithm is described. Phasing is performed viaab initio (e.g., Direct Methods, integrated by real space refinement) and non ab initio techniques (e.g., simulated annealing algorithm, when molecular geometry is a priori known). Some emphasis is given to running procedures: the main commands and directives are described, to allow the user to run default and non-default phasing attempts.

scholarly journals Structural study of decrespignyite-(Y), a complex yttrium rare earth copper carbonate chloride, by three-dimensional electron and synchrotron powder diffraction

2020 ◽  
Vol 32 (5) ◽  
pp. 545-555
Author(s):  
Jordi Rius ◽  
Fernando Colombo ◽  
Oriol Vallcorba ◽  
Xavier Torrelles ◽  
Mauro Gemmi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Rare Earth ◽  
Three Dimensional ◽  
South Australia ◽  
Direct Methods ◽  
Unit Cell ◽  
Synchrotron Powder Diffraction ◽  
Structure Solution ◽  
Hexanuclear Clusters ◽  
Metal Layers

Abstract. The crystal structure of the mineral decrespignyite-(Y) from the Paratoo copper mine (South Australia) has been obtained by applying δ recycling direct methods to 3D electron diffraction (ED) data followed by Rietveld refinements of synchrotron data. The unit cell is a= 8.5462(2), c= 22.731(2) Å and V= 1437.8(2) Å3, and the chemical formula for Z=1 is (Y10.35REE1.43Ca0.52Cu5.31)Σ17.61(CO3)14Cl2.21(OH)16.79⋅18.35H2O (REE: rare earth elements). The ED data are compatible with the trigonal P3‾m1 space group (no. 164) used for the structure solution (due to the disorder affecting part of the structure, the possibility of a monoclinic unit cell cannot completely be ruled out). The structure shows metal layers perpendicular to [001], with six independent positions for Y, REE and Cu (sites M1 to M4 are full, and sites M5 and M6 are partially vacant), and two other sites, Cu1 and Cu2, partially occupied by Cu. One characteristic of decrespignyite is the existence of hexanuclear (octahedral) oxo-hydroxo yttrium clusters [Y6(μ6-O)(μ3-OH)8O24] (site M1) with the 24 bridging O atoms belonging to two sets of symmetry-independent (CO3)2− ions, with the first set (2×) along a ternary axis giving rise to a layer of hexanuclear clusters and the second set (6×) tilted and connecting the hexanuclear clusters with hetero-tetranuclear ones hosting Cu, Y and REE (M2 and M3 sites). The rest of the crystal structure consists of two consecutive M3 + M4 layers containing the partially occupied M5, M6, and Cu2 sites and additional carbonate anions in between. The resulting structure model is compatible with the chemical analysis of the type material which is poorer in Cu and richer in (REE, Y) than the above-described material.

Automated diffraction tomography combined with electron precession: a new tool for ab initio nanostructure analysis

2009 ◽  
Vol 1184 ◽  
Author(s):  
Ute Kolb ◽  
Tatiana Gorelik ◽  
Enrico Mugnaioli
Keyword(s):  
Electron Diffraction ◽  
Ab Initio ◽  
Crystal Structures ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Direct Methods ◽  
Electron Diffraction Data ◽  
Diffraction Tomography ◽  
Diffraction Mode ◽  
Structure Solution

AbstractThree-dimensional electron diffraction data was collected with our recently developed module for automated diffraction tomography and used to solve inorganic as well as organic crystal structures ab initio. The diffraction data, which covers nearly the full relevant reciprocal space, was collected in the standard nano electron diffraction mode as well as in combination with the precession technique and was subsequently processed with a newly developed automated diffraction analysis and processing software package. Non-precessed data turned out to be sufficient for ab initio structure solution by direct methods for simple crystal structures only, while precessed data allowed structure solution and refinement in all of the studied cases.

SIR2004: an improved tool for crystal structure determination and refinement

2005 ◽  
Vol 38 (2) ◽  
pp. 381-388 ◽  
Author(s):  
Maria C. Burla ◽  
Rocco Caliandro ◽  
Mercedes Camalli ◽  
Benedetta Carrozzini ◽  
Giovanni L. Cascarano ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ab Initio ◽  
Structure Determination ◽  
Protein Structures ◽  
Medium Size ◽  
Graphical Interface ◽  
Asymmetric Unit ◽  
Density Maps ◽  
Data Resolution ◽  
User Friendly

SIR2004is the evolution of theSIR2002program [Burla, Camalli, Carrozzini, Cascarano, Giacovazzo, Polidori & Spagna (2003).J. Appl. Cryst.36, 1103]. It is devoted to the solution of crystal structures by direct and Patterson methods. Several new features implemented inSIR2004make this program efficient: it is able to solveab initioboth small/medium-size structures as well as macromolecules (up to 2000 atoms in the asymmetric unit). In favourable circumstances, the program is also able to solve protein structures with data resolution up to 1.4–1.5 Å, and to provide interpretable electron density maps. A powerful user-friendly graphical interface is provided.

The crystal structure of gatehouseite

2011 ◽  
Vol 75 (6) ◽  
pp. 2823-2832
Author(s):  
P. Elliott ◽  
A. Pring
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Three Dimensional ◽  
Direct Methods ◽  
Chemical Analyses ◽  
X Ray Diffraction ◽  
X Ray ◽  
Manganese Phosphate ◽  
Phosphate Mineral ◽  
Unit Formula

AbstractThe crystal structure of the manganese phosphate mineral gatehouseite, ideally Mn52+(PO4)2(OH)4, space group P212121, a = 17.9733(18), b = 5.6916(11), c = 9.130(4) Å, V= 933.9(4) Å3, Z = 4, has been solved by direct methods and refined from single-crystal X-ray diffraction data (T = 293 K) to an R index of 3.76%. Gatehouseite is isostructural with arsenoclasite and with synthetic Mn52+(PO4)2(OH)4. The structure contains five octahedrally coordinated Mn sites, occupied by Mn plus very minor Mg with observed <Mn—O> distances from 2.163 to 2.239 Å. Two tetrahedrally coordinated P sites, occupied by P, Si and As, have <P—O> distances of 1.559 and 1.558 Å. The structure comprises two types of building unit. A strip of edge-sharing Mn(O,OH)6 octahedra, alternately one and two octahedra wide, extends along [010]. Chains of edge- and corner-shared Mn(O,OH)6 octahedra coupled by PO4 tetrahedra extend along [010]. By sharing octahedron and tetrahedron corners, these two units form a dense three-dimensional framework, which is further strengthened by weak hydrogen bonding. Chemical analyses by electron microprobe gave a unit formula of (Mn4.99Mg0.02)Σ5.01(P1.76Si0.07(As0.07)Σ2.03O8(OH)3.97.

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