The crystal chemistry of Ti-rich trioctahedral micas of plutonic origin, cropping out at Black Hill (South Australia) has been investigated by combining electron microprobe analysis, single crystal X-ray diffraction, Mössbauer spectroscopy and X-ray photoelectron spectroscopy. Chemical analyses have shown the samples taken to be quite homogeneous and Ti-rich (TiO2 ≈ 7 wt.%). Mössbauer investigation yielded Fe2+/Fe3+ ≈ 30. X-ray photoelectron spectroscopy analysis seems to suggest the occurrence of three Ti species: octahedral Tr4+(60%), octahedral Ti3+(26%), and tetrahedral Ti4+(14%). The analyzed sample belongs to the 1M polytype and the relevant crystal data from structure analysis are: a = 5.347(1) Å, b = 9.261(2) Å, c = 10.195(2) Å, β = 100.29°(1). Anisotropic structure refinement was performed in space group C2/m, and converged at R = 2.62, Rw = 2.80. Structural details (the c cell parameter, the off-center shift of the M2 cation towards 04, the bond-length distortions of the cis-M2 octahedron, the interlayer sheet thickness, the projection of K−O4 distance along c*, the difference <K−O>outer-<K−O>inner) support the occurrence of the Ti-oxy substitution (VIR2+ + 2(OH)− ⇌ Ti4+ + 202− + H2) in the sample. Analysis of structural distortions as a function of the Ti content revealed that the positions of the oxygens 03 and 04 are displaced in opposite senses along [100]. This produces an enlargement of the M1 site with respect to the M2 site and a shortening of the interlayer distance. This trend seems to be in common with other Ti-rich 1M micas of plutonic origin.

The chemistry and the crystal structure of the recently described mineral argentopolybasite are critically discussed based on the study of two new occurrences of the mineral: Gowganda, Timiskaming District, Ontario, Canada and IXL Mine, Silver Mountain mining district, Alpine County, California.

The crystal structure of argentopolybasite can be described as the sequence, along the c axis, of two alternating layers: a [Ag6Sb2S7]2– A layer and a [Ag10S4]2+ B layer. In the B layer there are linearly-coordinated metal positions (B sites), which are usually occupied by copper in all members of the pearceite–polybasite group, resulting in a B-layer composition [Ag9CuS4]2+. In argentopolybasite, however, Ag fills all the metal sites in both A and B layers. By means of a multi-regression analysis on 67 samples of the pearceite–polybasite group, which were studied by electron microprobe and single-crystal X-ray diffraction, the effect of Ag, Sb and Se on the B sites of the B layer was modelled. Although the nomenclature rules for these minerals are based on chemical data only, we think this approach is useful to evaluate the goodness of the refinement of the structure (Ag/Cu disorder) and thus fundamental to discriminate different members of the pearceite–polybasite group.

Two tourmaline samples occurring in quartz veinlets, which cross-cut an amphibolite body at the Budniki camp near the Kowary town in the south-west part of the Karkonosze Mountains, SW Poland, were studied through microprobe and single crystal X-ray diffraction. Samples were extracted from core and rim regions of crystals with concentric zoning. Chemical and structural data revealed that the core tourmaline is characterised by a dravite–oxy-dravite composition, with the formula: X(Na0.82Ca0.07K0.01Sr0.01□0.09)Σ1Y(Mg1.73Fe2+0.81Fe3+0.41Ti0.04V0.01)Σ3Z(Al5.85Fe3+0.15)Σ6(TSi6O18)(BO3)3(OH)3W(OH0.50O0.50)Σ1 and unit cell parameters a = 15.97377(14) Å and c = 7.22644(7) Å. The rim part of the crystals has a magnesio-lucchesiite composition, described by the formula: X(Ca0.49Na0.41K0.04Sr0.02□0.04)Σ1Y(Mg1.87Fe2+0.95Ti0.15Fe3+0.02V0.02)Σ3Z(Al5.49Fe3+0.51)Σ6(BO3)3(TSi6O18)(OH)3W(O0.81F0.18OH0.01)Σ1 with unit cell parameters a = 15.9863(3) Å and c = 7.22426(15) Å. Both tourmalines show similar refined populations at the Y and Z sites: Y[(Fe2+0.810Mg0.680)Σ1.490(Al1.044Fe3+0.413V0.009)Σ1.465Ti0.045]Σ3Z(Al4.806Mg1.042Fe3+0.152)Σ6 (dravite–oxy-dravite), and Y[(Fe2+0.945Mg0.750)Σ1.695(Al0.737Fe3+0.404V0.018)Σ1.159Ti0.146]Σ3Z(Al4.749Mg1.115Fe3+0.137)Σ6 (magnesio-lucchesiite), with a comparable Mg/(Mg + Fe) ratio of ~0.54–0.56, oxidation of Fe expressed as Fe3+/Fetotal ratio ~0.36–0.41, and trace components such as Ti, Sr, V, Cr, Ni and Co. The geological history of the eastern Karkonosze region in the Kowary vicinity indicates that both tourmalines crystallised from B-bearing metamorphic fluids mobilised by Variscan prograde metamorphism from the protoliths of the Velká Upá mica schists that host the Budniki amphibolite. The fluids migrated into the tectonised amphibolite enriched in Ti, V, Cr, Ni and Co, and mineralised the fractures within it through deposition of soluble species in the form of quartz–tourmaline veinlets. Magnesio-lucchesiite crystallised in an early retrogression stage, probably from Ca- and F-bearing fluids secondary enriched in B by the dissolution of dravite–oxy-dravite. The Budniki camp is, in addition to the type and co-type magnesio-lucchesiite localities, the third documented occurrence of the species worldwide.

We report the crystal structure of allanite-(Ce), with composition (Ca1.0REE0.9□0.1)Σ2.0(Al1.46Fe3+0.52Fe2+0.76Mg0.12Ti0.15)Σ3.01Si3O12(OH) from the Xinfeng rare earth element (REE)-bearing granite in Guangdong Province, China. It has the unit cell a = 8.9550(4) Å, b = 5.77875(16) Å, c = 10.2053(4) Å, β = 114.929(5)° and Z = 2 in space group P21/m and is characterised by site splitting at M3 into M3a and M3b, at a distance of 0.38(3) Å, which are occupied partially by Fe0.764Mg0.12 and Ti0.15, respectively. The structure was determined by single-crystal X-ray diffraction and refined with anisotropic full-matrix least-squares refinement on F2 to R1 = 2.82%, wR2 = 7.77% for 1856 independent reflections (8772 collected reflections). However, M3 splitting is not present in either ferriallanite-(Ce) or epidote, in which M3 is almost fully occupied either by Fe2+ or by Fe3+. Comparisons of bond lengths and volumes in cation polyhedra among allanite-(Ce), ferriallanite-(Ce) and epidote tend to indicate that the essential factor that facilitates site splitting of M3 in allanite-(Ce) is heterovalent substitution and occupation of a crystallographic site between Fe2+(Mg2+/Mn2+)–Al3+(Ti4+), a common phenomenon in minerals, such as the plagioclase series. Fine structure analysis of the M3 split model revealed that deformation of A2 is related closely to distorted M3, which is consistent with Fe2+ incorporation following REE substitution.

The structural parameters of a second low-temperature form of KZnPO4 have been refined using Rietveld analysis of X-ray powder diffraction (XRPD) data. This form of KZnPO4 is isostructural with NH4ZnPO4I and has previously been denoted as KZnPO4II. This article uses the notation δ-KZnPO4, to be consistent with the α, β, and γ notation commonly used for other KZnPO4 phases.

Ludwigite from B-bearing iron ores in the Bergslagen area of central Sweden and in the coastal area north of Stockholm has been studied using chemical and single-crystal diffraction techniques. Structure refinements, completed for three crystals showing slightly different Al contents, in the space group Pbam (agreement factor: 2.42 ≤ R ≤ 2.79) indicate that: (1) octahedral M1, M2 and M3 bond distances are similar, although the calculated site population suggests that M1 and M2 are nearly completely occupied by Mg whereas M3 also contains Fe2+ and Fe3+; (2) in the M4 octahedron Fe3+ and Al dominate over Mg (and Fe2+); and (3) the distortion parameter, BLD, indicates that M3 is the most regular, whereas M4 is the most distorted octahedron.

Hyalotekite, a framework silicate of composition (Ba,Pb,K)4(Ca,Y)2Si8(B,Be)2 (Si,B)28F, is found in relatively high-temperature (⩾ 500°C) Mn skarns at Långban, Sweden, and peralkaline pegmatites at Dara-i-Pioz, Tajikistan. A new paragenesis at Dara-i-Pioz is pegmatite consisting of the Ba borosilicates leucosphenite and tienshanite, as well as caesium kupletskite, aegirine, pyrochlore, microcline and quartz. Hyalotekite has been partially replaced by barylite and danburite. This hyalotekite contains 1.29–1.78 wt.% Y2O3, equivalent to 0.172–0.238 Y pfu or 8–11% Y on the Ca site; its Pb/(Pb+Ba) ratio ranges 0.36–0.44. Electron microprobe F contents of Långban and Dara-i-Pioz hyalotekite range 1.04–1.45 wt.%, consistent with full occupancy of the F site. A new refinement of the structure factor data used in the original structural determination of a Långban hyalotekite resulted in a structural formula, (Pbl.96Bal.86K0.18)Ca2(B1.76Be0.24)(Sil.56B0.44)Si8O28F, consistent with chemical data and all cations with positive-definite thermal parameters, although with a slight excess of positive charge (+57.14 as opposed to the ideal +57.00). An unusual feature of the hyalotekite framework is that 4 of 28 oxygens are non-bridging; by merging these 4 oxygens into two, the framework topology of scapolite is obtained. The triclinic symmetry of hyalotekite observed at room temperature is obtained from a hypothetical tetragonal parent structure via a sequence of displacive phase transitions. Some of these transitions are associated with cation ordering, either Pb–Ba ordering in the large cation sites, or B–Be and Si–B ordering on tetrahedral sites. Others are largely displacive but affect the coordination of the large cations (Pb, Ba, K, Ca). High-resolution electron microscopy suggests that the undulatory extinction characteristic of hyalotekite is due to a fine mosaic microstructure. This suggests that at least one of these transitions occurs in nature during cooling, and that it is first order with a large volume change. A diffuse superstructure observed by electron diffraction implies the existence of a further stage of short-range cation ordering which probably involves both (Pb,K)–Ba and (BeSi,BB)–BSi.

Crystal structure refinements were performed on five Al-rich phlogopite-1M crystals (1.50 ⩽ Al3+ ⩽ 1.97 atoms per formula unit) from skarns of the Predazzo and Monzoni Hills petrographic area (north-east Italy) with the aim of characterizing geometrical variation produced by Al3+ increase. The charge imbalance was mostly compensated for by substitutions of highly charged cations in the octahedral sheet (Al3+ and/or Fe3+ for Mg2+). The refinements were carried out in the mean space group C2/m and gave agreement values (R) between 0.025 and 0.030. For some additional crystals, only chemistry and/or unit cell parameters were determined. In all samples the tetrahedra are more regular and larger than those previously reported in the literature for phlogopite crystals and the misfit between tetrahedral and octahedral sheets, produced by the increase in the tetrahedral edges, is mostly compensated for by the tetrahedral ring angle rotation α (10.2 °⩽ α ⩽ 12.5°), whereas the octahedral sheet features seem affected only by local crystal-chemical variations.

The first single-crystal structure refinement of aschamalmite (Pb6Bi2S9) from Susa Valley (Piedmont, Italy) is reported. The mineral is monoclinic, C2/m, a = 13.719(1) Å, b = 4.132(1) Å, c = 31.419(3) Å, β = 90.94(1)º, V = 1 780.8(4) A ˚3, Z = 4. The Pb6Bi2S9 compound crystallizes also in an orthorhombic form as heyrovskyite (Cmcm) and our study is focused on understanding the reason leading to a change in symmetry. The aschamalmite structure forms because of ordering between Pb and Bi on the margins of the two octahedral layers that are symmetrically equivalent in heyrovskyite. The two alternate set of octahedral slabs are not related by a crystallographic mirror plane and the symmetry decreases to monoclinic. The cation ordering couples opposite sequences of Pb and Bi octahedra at the margins of slabs. In particular,the succession [Me4A]Bi-[Me5A]Pb-[Me4A]Bi-[Me5A]Pb faced to the series [Me4B]Pb- [Me5B]Bi-[Me4B]Pb-[Me5B]Bi occurs in about 70% of the unit-cells of the crystal,while the contrary sequence ([Me4A]Pb-[Me5A]Bi-[Me4A]Pb-[Me5A]Bi faced to [Me4B]Bi-[Me5B]Pb-[Me4B]Bi-[Me5B]Pb) occurs in the remaining unit-cells. The marginal octahedra have ideal populations (a.p.f.u.): [Me4A]1.40Bi+0.60Pb, [Me4B]1.40Pb+0.60Bi, [Me5A]1.40Pb+0.60Bi, [Me5B]1.40Bi+0.60Pb,in agreement with our structurerefinement results.

The probable site populations for pure heyrovskyite have been proposed,as well as the reasons that prevent the formation of a completely ordered monoclinic phase.

A sample of the zeolite paulingite from the locality Vinarická Hora was investigated by means of chemical, thermal, powder and single crystal X-ray methods. The fully transparent, colourless to pale yellow crystals exhibit the form {110} and occur together with phillipsite. The chemical composition is (Ca2.57K2.28Ba1.39Na0.38)(Al11.55Si30.59O84)·27H2O, Z = 16 with minor amounts of Mg (<0.05), Sr (<0.13), Mn (<0.01), and Fe (<0.04). The chemical differences from previously described paulingites are a high Ba-content, a lower Si/(Al+Fe) ratio of 2.64, and a reduced water-content. The calculated density is 2.098 g cm−3, and the observed refractive index is 1.482(2). The dehydration behaviour is characterized by a main weight loss from 24–190°C (−11.2 wt.%, ≅ 21H2O) and a minor weight loss from 190–390°C (−3.1 wt.%, ≅ 6H2O). The rehydration capability was proven up to 150°C. The dehydration process during the main weight loss is accompanied by a reduction of the cell volume of 11%. The refined lattice parameters of the X-ray powder data are a a = 35.1231 (5) Å and a = 33.7485(8) Å of an untreated and a dehydrated sample, respectively. A breakdown of the paulingite structure can be observed while the remaining water content decomposes. The single crystal X-ray refinement of this chemically different sample material derived three main cation positions, which are inside a so called paulingite or π-cage (Ca), between 8-rings of neighbouring π-cages (Ba), and in the centre of the non-planar 8-rings of the γ-cage (K). Further partially occupied cation positions (Ca,Na) were located in the planar 8-rings of the α- and γ-cages. No positions within the double 8-membered rings were detected. The water is localized around the main cation positions and in three clusters of partially occupied sites.

Hydrothermal treatment of quartz with 2 M K2CO3 solutions at 623 K and 1 kbar resulted in the formation of single crystals of the monoclinic polymorph of potassium hydrogen disilicate (KHSi2O5 or KSi2O4(OH)). Basic crystallographic data of this so-called phase I at room conditions are as follows: space group C2/m, a = 14.5895(10) Å, b = 8.2992(3) Å, c = 9.6866(7) Å, β = 122.756(10)°, V = 986.36(10) Å3, Z = 8. The structure was determined by direct methods and refined to a residual of R(|F|) = 0.0224 for 892 independent observed reflections with I > 2σ(I). The compound belongs to the group of chain silicates. It is based on crankshaft-like vierer double-chains running parallel to [010]. The H atoms are associated with silanol groups. Hydrogen bonding between neighbouring double-chains results in the formation of ∼5 Å wide slabs. The three crystallographically independent K cations with six to eight O ligands provide linkage (1) between the chains of a single slab or (2) between adjacent slabs. Structural investigations have been supplemented by micro-Raman spectroscopy. The interpretation of the spectroscopic data including the allocation of the bands to certain vibrational species has been aided by DFT calculations.

The structure refinement of a hastingsite (Cl 0.91 p.f .u.) from West Ongul Island, Ltitzow-Holm Bay, East Antarctica, has been carried out in order to characterise the effect of CI on the crystal structure. The composition of the Cl-rich hastingsite is K0.69Na0.26Ca1.99Mg1.09Fe2+2.71Fe3+0.92Mn0.04Ti0.10−Al2.31Si5.83O22OH0.99Cl0.91F0.10 with unit cell parameters a 9.962(3), b 18.283(7), c 5.572(1) Å and β 104.87(3)°.

In the Cl-rich hastingsite, A1, Fe3+ and Ti occupy only the M(2) site, and Fe2+ strongly prefers the M(1) and M(3) sites to the M(2) site with respect to Mg. The Mg-Fe2+ distribution suggests that the Mg-CI avoidance is realised in the intracrystalline exchange reaction among the octahedral sites in the Cl-rich hastingsite. The individual position of CI and OH was refined and the effective ionic radius of Cl in fourfold coordination is determined as 1.79 Å. Substitution of Cl for OH expands the sizes of the M(1) and M(3) sites and extends the double chains in comparison with hydroxy calcic amphiboles. Cl especially, is close to the 0(6) and 0(7) oxygens beyond the minimum distance calculated from effective ionic radii. Therefore, the Cl-rich hastingsite is considered to be deformed locally by Cl.

The crystal chemistry of a meso-octahedral Li,Be-bearing mica from the Harding pegmatite (Dixon, Taos County, New Mexico, USA) has been investigated by constant-wavelength single-crystal neutron diffraction at 20 K, single-crystal X-ray diffraction at 100 K and inductively coupled plasma-atomic emission spectrometry (ICP-AES). The chemical composition based on ICP-AES analysis leads to the following chemical formula (calculated on the basis of 12 oxygen atoms): Ca(Na0.26K0.04Ca0.69)∑0.99M(Li0.29Mg0.03Fe0.023+Al1.78)∑2.12T(Al1.73Be0.16Si2.11)S4.00O12H2.53. The apparent excess of H is probably due to the fact that the fraction of H2O was assumed by difference to 100 wt.%, and slightly overestimated. On the basis of the previous experimental findings on Li,Be-bearing mica, X-ray (at 100 K) and neutron (at 20 K) structure refinements were performed in the space groups Cc and C2/c. The neutron structure refinement in the space group Cc offers a view about the (Al,Be,Si)-tetrahedral ordering: the best fit of the refinement was reached with the T1 and T4 sites occupied by (Be + Al) and T2 and T3 fully occupied by Si. This leads to a final population of T(Al1.88Be0.12Si2.00)∑4.00 p.f.u., in reasonable agreement with the chemical analysis. The neutron refinement provides unambigous evidence of the occurrence of Li at the M1 site. The refined fraction of Li at the M1 site ranges between 0.27 and 0.29 a.p.f.u., in excellent agreement with the chemical analysis. The presence of Li, at least at a significant level, at the M2 (and M3) site can be ruled out, as a full site occupancy with the scattering length of Al was obtained. The location of the H sites and the complex hydrogen-bonding scheme are described. A comparison between the structure features of this Li,Be-mica and other brittle micas is carried out.

The low-temperature structural behaviour of natural cancrinite with a formula Na6.59Ca0.93[Si6.12Al5.88O24](CO3)1.04F0.41·2H2O has been investigated by means of in situ single-crystal X-ray diffraction and Raman spectroscopy. High quality structure refinements were obtained at 293, 250, 220, 180, 140, 100 and at 293 K again (at the end of the low-T experiments). The variation in the unit-cell volume as a function of temperature (T) exhibits a continuous trend, without any evident thermoelastic anomaly. The thermal expansion coefficient αV = (1/V)∂V/∂T is 3.8(7) × 10–5 K–1 (between 100 and 293 K). The structure refinement based on intensity data collected at ambient conditions after the low-T experiment confirmed that the low-T induced deformation processes are completely reversible. The extraframework population does not show significant variations down to 100 K. The strong positional disorder of the carbonate groups along the c axis persists within the T range investigated. The structural behaviour of cancrinite at low-T is mainly governed by the continuous framework rearrangement through the ditrigonalization of the six-membered rings which lie in a plane perpendicular to [0001], the contraction of the four-membered ring joint units, the decrease of the ring corrugation in the (0001) plane, and the flattening of the cancrinite cages. A list of the principal Raman active modes in ambient conditions is provided and discussed.

Volcanic activity at Mt Vulture lasted throughout the Middle Pleistocene and produced SiO2- undersaturated volcanics. Deposits from the Monte Vulture stratovolcano have been classified into four subsynthems and clustered into the Barile Synthem. In the present investigation, trioctahedral micas from the uppermost units (the Ventaruolo Subsynthem) of the Barile Synthem are considered. The samples are labelled VUT187. The phlogopitic micas were separated from the host rock (an olivinefoidite) and underwent chemical (electron microprobe analysis - EMPA and C-H-N), structural (singlecrystal X-ray diffraction) and spectroscopic (Mössbauer) investigations.

The EMPA yielded: MgO (17.62–21.89 wt.%), FeOtot (5.98–9.78 wt.%), TiO2 (1.81–3.92 wt.%) and Al2O3 (14.47–17.98 wt.%), with H2O contents = 2.86 (±0.42) wt.% determined by C-H-N analyses. Mössbauer investigation provided [VI]Fe2+ = 12.6%, [VI]Fe3+ = 87.4%. The chemical and structural data are consistent with the occurrence of Ti-oxy, [VI]M2+ + 2(OH)– ⇋ [VI]Ti4+ + 2O2– + H2, and M3+-oxy substitutions, [VI]M2+ + (OH)– ⇋ [VI]M3+ + O2– + 1/2H2, with M3+ = Fe3+, Al3+. In particular, Fe3+-oxy substitution has affected the Fe2+/Fe3+ ratioin the studied sample. This is probably due to the fact that interaction with underground water or a hydrothermal system may have altered the oxygen fugacity and raised the Fe3+ content of VUT187 phlogopite with respect to magmatic values.

New chemical (EMP, SIMS) and structural data are reported for a suite of crystals of oxo-mangani-leakeite and mangano-mangani-ungarettiite from their common type locality, the Hoskins mine (New South Wales, Australia). Notwithstanding the low OH content, FTIR analysis of selected sampleshas provided considerable information on short-range order in these Mn3+-rich amphiboles, and shows that Li is associated with occupied A sites and is linked to the oxo-component at the O(3) site. Comparative analysis of all available data allows us to: (1) further improveour understanding of the crystal-chemistry of these very peculiar compositions of the oxo-amphibole group; and (2) calculate reliable site-populations. The proposed limited compositional variability has been confirmed. The two amphiboles have completely different arrangements of CR3+cations. In oxo-mangani-leakeites, those CR3+ cations related to the oxocomponent occur at the M (1) site, whereas those CR3+ cations related to the leakeite charge-arrangement occur at the M (2) site. In mangano-mangani-ungarettiite,all CR3+ cations order at the M (1) and M (3) sites, and local bond-valence requirements are satisfied by the presence of Mn3+, which assumes a strongly distorted coordination due to its degenerate eg electronic state. Therefore,the inverse patterns observed for both cation-ordering and deformation of the octahedra are incompatible with solid-solution between these two species that coexist at the Hoskins mine.

Surface roughness of planar samples causes an additional attenuation of X-ray diffraction intensity measured in Bragg–Brentano geometry. The decrease of intensity becomes stronger with decreasing scattering angle. This is part of the microabsorption effect. Two quantitative expressions describing the microabsorption effect are incorporated into the DBWS 9006-PC Rietveid program [D. B. Wiles and R. A. Young, J. Appl. Crystallogr. 15, 149–151 (1981)]. The procedure is applied to scattering data obtained from YBa2Cu3O7-powder samples with different degree of surface roughness but approximately identical bulk structure. The procedure is proved to work well. However, the values obtained for the parameters of the temperature factors and the microabsorption effect are correlated, and careful discussion is necessary to interpret the results.

The kalipyrochlore (K,Sr,Na,Ca,H2O)2−m(Nb,Ti)2−xO6−wY1−n, with (0<m<0.8, x∼0.2, w = 0 and 0.2<n<1) from Lueshe, Zaire is a defect pyrochlore species whose A-site weakly depleted. The measured powder diffraction is presented with a calculated figure of merit F(30) = 74.7(0.010,39). The structure has been refined by single-crystal from X-ray diffraction data collected on a Huber four-circle diffractometer and by Rietveld analysis from X-ray powder diffraction data. The slightly weathered crystal (studied by single crystal) has a cubic pyrochlore-type structure with the same atomic positions and a unit-cell parameter a = 10.603(5) Å, space group (S.G.): Fd3m. The highly weathered crystal (studied by Rietveld) has the same cubic pyrochlore-type structure except for the oxygen position. The oxygen moved from the 48f position with x, y, z equal to 0.284, 0, 0 to x = 0.308(5), y = 0.024(6) and z = –0.028(9). The cell parameter is a = 10.569(6)±0.0007 Å. These modifications of positions induce a distortion of the A-site into an hexagonal bipyramid and an elongation of the B-site along the c axis of the octahedron.

The accelerated pace of genomic sequencing has increased the demand for structural models of gene products. Improved quantitative methods are needed to study the many systems (e.g., macromolecular assemblies) for which data are scarce. Here, we describe a new molecular dynamics method for protein structure determination and molecular modeling. An energy function, or database potential, is derived from distributions of interatomic distances obtained from a database of known structures. X-ray crystal structures are refined by molecular dynamics with the new energy function replacing the Van der Waals potential. Compared to standard methods, this method improved the atomic positions, interatomic distances, and side-chain dihedral angles of structures randomized to mimic the early stages of refinement. The greatest enhancement in side-chain placement was observed for groups that are characteristically buried. More accurate calculated model phases will follow from improved interatomic distances. Details usually seen only in high-resolution refinements were improved, as is shown by an R-factor analysis. The improvements were greatest when refinements were carried out using X-ray data truncated at 3.5 Å. The database potential should therefore be a valuable tool for determining X-ray structures, especially when only low-resolution data are available.