Corrigenda for five articles.
The affiliation of one of the authors and a source of funding are both added in the following papers: Chiririwa & Meijboom [Acta Cryst. (2011a), E67, m1496; Acta Cryst. (2011b), E67, m1497; Acta Cryst. (2011c), E67, m1498] and Chiririwa & Muller [Acta Cryst. (2012a), E68, m49; Acta Cryst. (2012b), E68, m116–m117].
To determine the effect of an endothelin type A receptor antagonist (ETA) on uterine artery resistive index (UARI) and mean arterial pressure (MAP) in a placental ischemia rat model of pre-eclampsia produced by Reductions in Uterine Perfusion Pressure (RUPP).
UARI was assessed by Doppler velocimetry in the RUPP and normal pregnant controls (NP) on gestation days (GD) 12, 15 and 18. UARI was also determined on GD 18 in NP and RUPP pregnant dams after pretreatment with ETA. MAP was recorded on GD 19.
The RUPP group had a higher MAP and UARI on GD 15 and 18 than the NP group. Pretreatment with ETA attenuated both the MAP and GD 18 UARI in the RUPP group without affecting these parameters in the NP group.
The improvement in UARI could be one potential mechanism for the reduction in MAP in response to ETA in pregnant dams with ischemic placentas.
Doppler velocimetry; Uterine artery resistive index; Endothelin type A receptor antagonist; hypertension; preeclampsia
The article by Natarajan & Mathews [(2012) (2012) Acta Cryst. F68, 207–210] is retracted.
The article by Natarajan & Mathews [(2012) Acta Cryst. F68, 207–210] is retracted.
Pseudomonas aeruginosa; aspartyl aminopeptidase; retraction
The accuracy of a dispersion-corrected density functional theory method is validated against 241 experimental organic crystal structures from Acta Cryst. Section E.
This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.
dispersion-corrected density functional theory; organic structures
A corrigendum to the article by Dutta et al.
[(2012) Acta Cryst. F68, 786–789].
In the article by Dutta et al. [(2012) Acta Cryst. F68, 786–789] two citations were given erroneously. These are now corrected.
FabG4; high-molecular-weight ketoacyl reductases; Mycobacterium tuberculosis; corrigendum
An addendum to the article by Do et al. [(2012) Acta Cryst. F68, 806–809].
An additional acknowledgement is published for the article by Do et al. [(2012) Acta Cryst. F68, 806–809].
antifreeze proteins; ice-binding proteins; Flavobacterium frigoris PS1; psychrophilic bacteria; addendum
Corrigendum to Acta Cryst. (2012), E68, m1025.
The author list in the paper by Mafud [Acta Cryst. (2012), E68, m1025] is corrected.
In the crystal structure of the title compound, C16H14F3N3OS·C3H8O, the molecules are linked into chains along  via N—H⋯O and O—H⋯N hydrogen bonds. The triclinic form was reported by Ren et al. [(2011). Acta Cryst. E67, o270] and the first monoclinic form by Chen et al. [(2012). Acta Cryst. E68, o2015–o2016]. The fused five-and six-membered rings make a dihedral angle of 1.22 (2)°, while the benzene and pyridine rings make a dihedral angle of 10.15 (2)°.
Birch pollen is one of the main causes of allergy during spring and early summer in northern and central Europe. The aim of this study was to create a forecast model that can accurately predict daily average concentrations of Betula sp. pollen grains in the atmosphere of Szczecin, Poland. In order to achieve this, a novel data analysis technique—artificial neural networks (ANN)—was used. Sampling was carried out using a volumetric spore trap of the Hirst design in Szczecin during 2003–2009. Spearman’s rank correlation analysis revealed that humidity had a strong negative correlation with Betula pollen concentrations. Significant positive correlations were observed for maximum temperature, average temperature, minimum temperature and precipitation. The ANN resulted in multilayer perceptrons 366 8: 2928-7-1:1, time series prediction was of quite high accuracy (SD Ratio between 0.3 and 0.5, R > 0.85). Direct comparison of the observed and calculated values confirmed good performance of the model and its ability to recreate most of the variation.
Birch; Artificial neural network; Meteorological parameter; Forecast model
A corrigendum to the article by Inoguchi et al. [(2013). Acta Cryst. F69, 393–398].
The affiliation of two authors in the article by Inoguchi et al. [(2013). Acta Cryst. F69, 393–398] is corrected.
hemoglobin; deer mouse; oxygen affinity; Peromyscus maniculatus; corrigendum
A corrigendum to the article by Najmudin et al. [Acta Cryst. (2009). F65, 730–732].
A correction is made to the name of one of the authors in the article by Najmudin et al. [Acta Cryst. (2009). F65, 730–732].
mixed-metal sulfide cluster; Desulfovibrio gigas; molybdenum; copper; corrigendum
An addition to the paper by Cheng et al. [(2010), Acta Cryst. F66, 546–548].
An author is added to the article by Cheng et al. [(2010), Acta Cryst. F66, 546–548].
A corrigendum to the article by Ito et al. [Acta Cryst. (2008). F64, 531–532].
A correction is made to the list of authors for Ito
et al. [Acta Cryst. (2008). F64, 531–532].
prouroguanylin; precursor proteins; peptide hormones; corrigendum
Preeclampsia is associated with innate inflammatory response resulting in elevated TNF alpha, agonistic autoantibodies to the angiotensin II type I receptor (AT1-AA) and activation of endothelin-1 (ET-1). This study was designed to determine the role of B cell depletion, resulting AT1-AA suppression to mediate hypertension via activation of ET-1 in placental ischemic RUPP rat model of preeclampsia. To achieve this goal we examined the effect of RUPP on MAP and ET-1 in the presence and absence of chronically infused Rutiximab (R) (250mg/kg), a B lymphocyte suppressive agent used clinically to treat autoimmune diseases. Blood pressure (MAP) was 103 +/− 1 mmHg in NP;103 +/− 3 mmHg in NP+R vs 133 +/−2 mmHg in RUPP rats and 118 +/−2 mmHg in RUPP+R (p<0.001vs RUPP controls). B lymphocytes decreased from 6.0 +/−0.5% in RUPP to 3.7 +/−0.8 % gated cells in RUPP+R. Importantly, AT1-AA decreased from 18+/−1 in RUPP to 10+/−1bpm in RUPP+R. ET-1 decreased 1.5 fold in kidneys and 4 fold in placenta (P<0.01) of RUPP+R vs RUPP. Media ET-1 excretion from endothelial cells exposed to serum from NP, RUPP, NP+R or RUPP+R rats was determined. ET-1 from endothelial cells treated with NP serum was 53+13pg/mg and increased to 75+10pg/mg with RUPP serum. In contrast ET-1 secretion decreased in response to B cell depleted RUPP serum to 50+/−8pg/mg, and was unchanged in response to NP+R sera (46+/−12 pg/mg). These data demonstrate the important role that B lymphocyte activation and AT1-AAs play in the pathophysiology of hypertension in response to placental ischemia.
Hypertension; inflammation; renin-angiotensin system; pregnancy; endothelin
The etiology of preeclampsia remains unknown. However, a contributing factor to this hypertensive disease of pregnancy is a reduction in uterine perfusion pressure resulting in placental ischemia. Uterine arteries may be a major regulator of this process through changes in vascular reactivity and localized blood flow. The reduced uterine perfusion pressure (RUPP) pregnant rat is an established animal model of preeclampsia pathology. Pregnant Sprague Dawley rats were used for this investigation and subjected to RUPP or SHAM surgery on Day 14 of gestation. On Day 21 of gestation, animals were terminated and resistance-caliber uterine arteries were harvested and mounted on a pressurized arteriograph to examine myogenic reactivity, agonist induced vasodilation (methacholine and VEGF), and vasoconstriction (phenylephrine and U-46619). Resistance-caliber uterine arteries from RUPP animals exhibited increased myogenic reactivity and decreased vasodilation (methacholine and VEGF) compared to SHAM uterine arteries (p<0.05). Phenylephrine and U-46619 induced constriction was similar in uterine arteries between RUPP and SHAM rats. These results suggest that resistancecaliber uterine arteries from RUPP pregnant rats are altered to reflect a more constrictive phenotype which may play a role in the development of maternal hypertension demonstrated in these animals and thereby potentially in preeclampsia.
Preeclampsia; uterine artery; myogenic reactivity; RUPP; vasodilation
A correction to the paper by Asojo et al. [(2005), Acta Cryst. F61, 391–394].
Data collection and instrument information reported in the article by Asojo et al. [(2005), Acta Cryst. F61, 391–394] are corrected.
pathogenesis-related proteins; hookworm; ASP; Necator americanus; ancylostoma; vaccines; erratum
The crystal structure of dizinc trimolybdenum(IV) octaoxide, Zn2Mo3O8, has been redetermined from single-crystal X-ray data. The structure has been reported previously based on neutron powder diffraction data [Hibble et al. (1999 ▶). Acta Cryst. B55, 683-697] and single-crystal data [McCarroll et al. (1957 ▶). J. Am. Chem. Soc.
79, 5410–5414; Ansell & Katz (1966 ▶) Acta Cryst.
21, 482–485]. The results of the current redetermination show an improvement in the precision of the structural and geometric parameters with all atoms refined with anisotropic displacement parameters. The crystal structure consists of distorted hexagonal-close-packed oxygen layers with stacking sequence abac along  and is held together by alternating zinc and molybdenum layers. The Zn atoms occupy both tetrahedral and octahedral interstices with a ratio of 1:1. The Mo atoms occupy octahedral sites and form strongly bonded triangular clusters involving three MoO6 octahedra that are each shared along two edges, forming a Mo3O13 unit. All atoms lie on special positions. The Zn atoms are in 2b Wyckoff positions with 3m. site symmetry, the Mo atoms are in 6c Wyckoff positions with . m. site symmetry and the O atoms are in 2a, 2b and 6c Wyckoff positions with 3m. and . m. site symmetries, respectively.
Corrigendum to Acta Cryst. (2009), E65, o301.
Consideration of a previous unrecognized twinning of the original investigated crystal of the title compound [Kia et al. (2009 ▶). Acta Cryst. E65, o301] led to improved reliability factors and to a slightly higher precision for all geometric parameters. The crystal under investigation was twinned by pseudo-merohedry with [100, 00, 00] as the twin matrix and a refined twin domain fraction of 0.9610 (5):0.0390 (5). The results of the new crystal structure refinement are given here.
In the six-membered ring of the low-temperature crystal structure of benzofurazan 1-oxide, C6H4N2O2, the two C atoms adjacent to the N atoms are linked by a delocalized aromatic bond [1.402 (2) Å]; each is connected to its neighbour by a longer, more localized, bond [1.420 (2), 1.430 (2) Å]. However, the next two bonds in the ring approximate double bonds [1.357 (2), 1.366 (2) Å]. As such, the six-membered ring is better described as a cyclohexadiene system, in contrast to the description in the room-temperature structure reported by Britton & Olson (1979 ▶) [Acta Cryst. B35, 3076–3078].
The title salt, C12H24N+·NCS−, represents a monoclinic polymorph of the previously reported orthorhombic form [Khawar Rauf et al. (2008 ▶). Acta Cryst. E64, o366]. Two independent formula units comprise the asymmetric unit with the major difference in their molecular structures relating to the relative dispositions of the cyclohexyl rings [dihedral angles = 79.88 (6) and 67.72 (5)°]. Further, the independent anions form distinctive patterns of hydrogen-bonding interactions, i.e. 2 × N—H⋯N versus N—H⋯N and N—H⋯S. The resulting supramolecular architecture is a supramolecular chain along the c axis based on a square-wave topology.
The angle τ (backbone N—Cα—C) is the most contested Engh and Huber refinement target parameter. It is shown that this parameter is ‘correct’ as a PDB-wide average, but can be improved by taking into account residue types, secondary structures and many other aspects of our knowledge of the biophysical relations between residue type and protein structure.
The Engh and Huber parameters for bond lengths and bond angles have been used uncontested in macromolecular structure refinement from 1991 until very recently, despite critical discussion of their ubiquitous validity by many authors. An extensive analysis of the backbone angle τ (N—Cα—C) illustrates that the Engh and Huber parameters can indeed be improved and a recent study [Tronrud et al. (2010 ▶), Acta Cryst. D66, 834–842] confirms these ideas. However, the present study of τ shows that improving the Engh and Huber parameters will be considerably more complex than simply making the parameters a function of the backbone ϕ, ψ angles. Many other aspects, such as the cooperativity of hydrogen bonds, the bending of secondary-structure elements and a series of biophysical aspects of the 20 amino-acid types, will also need to be taken into account. Different sets of Engh and Huber parameters will be needed for conceptually different refinement programs.
protein structure; protein geometry; stereochemical parameters; restraints; N—Cα—C bond angle
The crystallization and preliminary neutron crystallographic analysis of selectively CH3-protonated deuterated rubredoxin from P. furiosus is presented. This work represents the first reported use of selectively labeled material for phasing applications using neutron protein crystallography.
Neutron crystallography is used to locate H atoms in biological materials and can distinguish between negatively scattering hydrogen-substituted and positively scattering deuterium-substituted positions in isomorphous neutron structures. Recently, Hauptman & Langs (2003 ▶; Acta Cryst. A59, 250–254) have shown that neutron diffraction data can be used to solve macromolecular structures by direct methods and that solution is aided by the presence of negatively scattering H atoms in the structure. Selective-labeling protocols allow the design and production of H/D-labeled macromolecular structures in which the ratio of H to D atoms can be precisely controlled. Methyl selective-labeling protocols were applied to introduce (1H-δ methyl)-leucine and (1H-γ methyl)-valine into deuterated rubredoxin from Pyrococcus furiosus (PfRd). Here, the production, crystallization and preliminary neutron analysis of a selectively CH3-protonated deuterated PfRd sample, which provided a high-quality neutron data set that extended to 1.75 Å resolution using the new LADI-III instrument at the Institut Laue-Langevin, are reported. Preliminary analysis of neutron density maps allows unambiguous assignment of the positions of H atoms at the methyl groups of the valine and leucine residues in the otherwise deuterated rubredoxin structure.
rubredoxin; deuteration; selective labeling; neutron diffraction
The crystal structure of bis(2-formylphenolato-κ2
O,O′)nickel(II), [Ni(C7H5O2)2], a square-planar centrosymmetric complex, has been reported previously [Li & Chen (2006). Acta Cryst. E62, m1038–m1039]. However, a number of warning signs allows the assumption that the carbonyl group in the salicylaldehydate ligand of the claimed complex is incorrect. The crystal structure was therefore redetermined on basis of the originally deposited structure factors. After substituting the carbonyl O atom by an N atom, the model can be completed with an imine H atom, which was clearly discernible in a difference map. The resulting model, corresponding to bis[2-(iminomethyl)phenolato-κ2
N,O′]nickel(II), [Ni(C7H6NO)2], converges well and none of the previous structural alerts remains. This reinterpretation is also consistent with the published synthesis, which was carried out using salicylaldehyde in the presence of aqueous NH3. The reinterpreted structure is virtually identical to earlier reports dealing with this bis-iminato NiII complex.
The crystal structure of the title compound [systematic name: 5,6,10-trihydroxy-7-isopropyl-1,1,4a-trimethyl-2,3,4,4a-tetrahydrophenanthren-9(1H)-one], C20H26O4, has been reported previously [Salae et al. (2009 ▶). Acta Cryst. E65, o2379–o2380], but the absolute configuration could not be determined as there was no significant anomalous dispersion using data collected with Mo radiation. The absolute configuration has now been determined by refinement of the Flack parameter with data collected using Cu radiation. The absolute configuration at position 4a of the diterpenoid is (R)-methyl; other features of the molecule and its crystal packing are similar to those previously described.
The crystal structure of the title compound, [Sn(C5H10NS2)4], was originally determined by Harreld & Schlemper [Acta Cryst. (1971), B27, 1964–1969] using intensity data estimated from Weissenberg films. In comparison with the previous refinement, the current redetermination reveals anisotropic displacement parameters for all non-H atoms, localization of the H atoms, and higher precision of lattice parameters and interatomic distances. The complex features a distorted S6 octahedral coordination geometry for tin and a cis disposition of the monodentate dithiocarbamate ligands.