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1.  Crystallization and preliminary X-ray analysis of ginkbilobin-2 from Ginkgo biloba seeds: a novel antifungal protein with homology to the extracellular domain of plant cysteine-rich receptor-like kinases. Erratum 
An erratum to the paper by Miyakawa et al. [(2007), Acta Cryst. F63, 737–739].
A correction is made to one of the affiliations of the authors and also to a table heading in Miyakawa et al. (2007), Acta Cryst. F63, 737–739.
PMCID: PMC2339736
ginkbilobin-2; antifungal proteins; Ginkgo biloba; erratum
2.  Strontium tetra­fluoro­borate. Erratum 
Erratum to Acta Cryst. (2007), C63, i75–i76.
In the paper by Bunič, Tavčar, Goreshnik & Žemva [Acta Cryst. (2007 ▶), C63, i75–i76], the structure reported as Sr(BF4)2 is actually that of Cd(BF4)2. The correct structure of Sr(BF4)2 is now reported.
PMCID: PMC2855578
3.  Expression, purification, crystallization and preliminary X-ray diffraction analysis of galactokinase from Pyrococcus horikoshii. Erratum 
An erratum to the paper by Inagaki et al. [(2006), Acta Cryst. F62, 169–171].
An error is corrected in the paper by Inagaki et al. [(2006), Acta Cryst. F62, 169–171].
PMCID: PMC2197199
galactokinase; Leloir pathway; glycolysis; Pyrococcus horikoshii
4.  (4S,5R,6R)-Methyl 4-hydr­oxy-4,5-iso­propyl­idenedioxy-4,5,6,7-tetra­hydro-1,2,3-triazolo[1,5-a]pyridine-3-carboxyl­ate. Erratum 
Corrigendum to Acta Cryst. (2009), E65, o610–o611.
The chemical name of the title compound in the paper by Jenkinson, Fenton, Booth, Fleet & Watkin [Acta Cryst. (2009), E65, o610–o611] is corrected.
PMCID: PMC2970035  PMID: 21577385
5.  The active site of hen egg-white lysozyme: flexibility and chemical bonding 
Chemical bonding at the active site of lysozyme is analyzed on the basis of a multipole model employing transferable multipole parameters from a database. Large B factors at low temperatures reflect frozen-in disorder, but therefore prevent a meaningful free refinement of multipole parameters.
Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader’s quantum theory of atoms in molecules [QTAIM; Bader (1994 ▶), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254–1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337–351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C—H⋯O hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.
PMCID: PMC3975892  PMID: 24699657
hen egg-white lysozyme; multipole model; multipole parameters
6.  Poly[μ2-chlorido-nona­methyl-μ3-nitrato-tritin(IV)]. Corrigendum 
Corrigendum to Acta Cryst. (2007), E63, m2329.
An error in the original formulation of the title compound in the paper by Sadiq-ur-Rehman, Sherzaman, Ali, Shahzadi & Helliwell [Acta Cryst. (2007), E63, m2329] is corrected.The title compound in the paper by Sadiq-ur-Rehman, Sherzaman, Ali, Shahzadi & Helliwell [Acta Cryst. (2007), E63, m2329] was an unexpected product which seemed to have nitrate coordinated to three Sn atoms. However, it was noticed that the charges do not balance and that it is most likely that the nitrate is in fact a carbonate. Regrettably, there is no material to carry out microanalysis, but a plausible mechanism has been suggested to explain the unexpected formation of the product. Trimethyl­tin chloride will react with methanol in the presence of a base (4-hydroxy­piperidine) to give trimethyl­tin methoxide, which will rapidly hydrolyze in air to give the hydroxide. Both the methoxide and the hydroxide will react with atmospheric CO2 to give the carbonate (Bloodworth et al., 1967 ▶; Blunden et al., 1984 ▶; Sato, 1967 ▶). Me3SnCl + MeOH + base → Me3SnOMe + base·HCl Me3SnOMe + H2O → Me3SnOH + MeOH Me3SnOH + CO2 → Me3SnOCO2HMe3SnOCO2H + Me3SnOMe → Me3SnOCO2SnMe3 + MeOH. The carbonate then forms a coordination copolymer with trimethyl­tin chloride. The name of the title compound is corrected to poly[μ3-carbonato-μ3-chlorido-nona­methyl­tri­tin(IV)], [Sn3(CH3)9(CO3)Cl] (M r = 586.84).
PMCID: PMC2961754  PMID: 21202727
7.  Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations 
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.
PMCID: PMC2940256  PMID: 20841921
dispersion-corrected density functional theory; organic structures
8.  Distinguishing tautomerism in the crystal structure of (Z)-N-(5-ethyl-2,3-di­hydro-1,3,4-thia­diazol-2-yl­idene)-4-methyl­benzene­sulfonamide using DFT-D calculations and 13C solid-state NMR 
The crystal structure of (Z)-N-(5-ethyl-2,3-di­hydro-1,3,4-thia­diazol-2-yl­idene)-4-methyl­benzene­sulfonamide contains an imine tautomer, rather than the previously reported amine tautomer. The tautomers can be distinguished using dispersion-corrected density functional theory calculations and by comparison of calculated and measured 13C solid-state NMR spectra.
The crystal structure of the title compound, C11H13N3O2S2, has been determined previously on the basis of refinement against laboratory powder X-ray diffraction (PXRD) data, supported by comparison of measured and calculated 13C solid-state NMR spectra [Hangan et al. (2010 ▶). Acta Cryst. B66, 615–621]. The mol­ecule is tautomeric, and was reported as an amine tautomer [systematic name: N-(5-ethyl-1,3,4-thia­diazol-2-yl)-p-toluene­sulfonamide], rather than the correct imine tautomer. The protonation site on the mol­ecule’s 1,3,4-thia­diazole ring is indicated by the inter­molecular contacts in the crystal structure: N—H⋯O hydrogen bonds are established at the correct site, while the alternative protonation site does not establish any notable inter­molecular inter­actions. The two tautomers provide essentially identical Rietveld fits to laboratory PXRD data, and therefore they cannot be directly distinguished in this way. However, the correct tautomer can be distinguished from the incorrect one by previously reported qu­anti­tative criteria based on the extent of structural distortion on optimization of the crystal structure using dispersion-corrected density functional theory (DFT-D) calculations. Calculation of the 13C SS-NMR spectrum based on the correct imine tautomer also provides considerably better agreement with the measured 13C SS-NMR spectrum.
PMCID: PMC4174016  PMID: 25093360
crystal structure; powder diffraction; NMR analysis; amine–imine tautomerism; dispersion-corrected DFT
9.  Poly[[tetra-μ2-aqua-diaqua-μ6-oxalato-barium(II)] 2,4,6-trinitro­phenolate monohydrate]. Corrigendum 
Corrigendum to Acta Cryst. (2007), E63, o2296.
In the paper by Hong, Song & Wu [Acta Cryst. (2007), E63, o2296], the scheme shows the wrong structure. The correct scheme is shown below and the compound name is corrected to "poly[[di-μ2-aqua-diaqua-hemi-μ6-oxalato-barium(II)] 2,4,6-trinitro­phenolate monohydrate", {[Ba(C2O4)0.5(H2O)4]C6H2N3O7·H2O}n.
PMCID: PMC2914902  PMID: 21200449
10.  Diholmium(III) tris­ulfate tetra­hydrate. Corrigendum 
Corrigendum to Acta Cryst. (2007), E63, i194.
The title and formula in the paper by Zhou et al. [Acta Cryst. (2007), E63, i194] are corrected.
PMCID: PMC3414092
11.  Seven papers on fused-ring heterocyclic ketones containing an N-tosyl­pyrrolo­[3,4-c]pyrano moiety. Corrigenda 
Corrigenda to Acta Cryst. (2007), E63, o4363, o4364, o4434–o4435, o4436–o4437, o4438, o4489–o4490 and o4491–o4492.
Corrections are made to the name of an author in seven papers by Chinnakali et al. [Acta Cryst. (2007), E63, o4363, o4364, o4434–o4435, o4436–o4437, o4438, o4489–o4490 and o4491–o4492].
PMCID: PMC2914901  PMID: 21200448
12.  3-Acetyl-4-hydroxy­phenyl acrylate. Corrigendum 
Corrigendum to Acta Cryst. (2007), E63, o4725.
The chemical name in the title of the paper by Chakkara­varthi, Anthonysamy, Balasubramanian & Manivannan [Acta Cryst. (2007), E63, o4725] is corrected.
PMCID: PMC2959737  PMID: 21580807
13.  2-[4-(Diethyl­amino)phen­yl]-1-ethyl­imidazo[4,5-f][1,10]­phenanthroline. Corrigendum 
Corrigendum to Acta Cryst. (2007), E63, o1210–o1211.
The list of authors in the paper by Sun, Chen, Ling & Liu [Acta Cryst. (2007), E63, o1210–o1211] is corrected.
PMCID: PMC2960653  PMID: 21201562
14.  4-[3-(Chloro­meth­yl)-1,2,4-oxadiazol-5-yl]pyridine. Corrigendum 
Corrigendum to Acta Cryst. (2007), E63, o4654.
The title and the chemical diagram of the paper by Kang, Li, Zeng, Wang & Wang [Acta Cryst. (2007), E63, o4654] are corrected.
PMCID: PMC2961134  PMID: 21202159
15.  (Z)-1,2-Bis(4-nitro­phen­yl)ethene. Corrigendum 
Corrigendum to Acta Cryst. (2007), E63, o3999.
The name of the first author in the paper by Chen & Cao [Acta Cryst. (2007), E63, o3999] is corrected.
PMCID: PMC2961310  PMID: 21202160
16.  Reinvestigation of bis­(2,2′-bipyridine)(nitrato-κ2 O,O′)cobalt(III) hydroxide nitrate tetra­hydrate. Corrigendum 
Corrigendum to Acta Cryst. (2007), E63, m2975–m2976.
The chemical formula in the paper by Wojciechowska & Daszkiewicz [Acta Cryst. (2007), E63, m2975–m2976] is corrected.
PMCID: PMC3011626  PMID: 21589198
17.  Assessment of radiation damage behaviour in a large collection of empirically optimized datasets highlights the importance of unmeasured complicating effects 
Journal of Synchrotron Radiation  2011;18(Pt 3):387-397.
A retrospective analysis of radiation damage behaviour in a statistically significant number of real-life datasets is presented, in order to gauge the importance of the complications not yet measured or rigorously evaluated in current experiments, and the challenges that remain before radiation damage can be considered a problem solved in practice.
The radiation damage behaviour in 43 datasets of 34 different proteins collected over a year was examined, in order to gauge the reliability of decay metrics in practical situations, and to assess how these datasets, optimized only empirically for decay, would have benefited from the precise and automatic prediction of decay now possible with the programs RADDOSE [Murray, Garman & Ravelli (2004 ▶). J. Appl. Cryst. 37, 513–522] and BEST [Bourenkov & Popov (2010 ▶). Acta Cryst. D66, 409–419]. The results indicate that in routine practice the diffraction experiment is not yet characterized well enough to support such precise predictions, as these depend fundamentally on three interrelated variables which cannot yet be determined robustly and practically: the flux density distribution of the beam; the exact crystal volume; the sensitivity of the crystal to dose. The former two are not satisfactorily approximated from typical beamline information such as nominal beam size and transmission, or two-dimensional images of the beam and crystal; the discrepancies are particularly marked when using microfocus beams (<20 µm). Empirically monitoring decay with the dataset scaling B factor (Bourenkov & Popov, 2010 ▶) appears more robust but is complicated by anisotropic and/or low-resolution diffraction. These observations serve to delineate the challenges, scientific and logistic, that remain to be addressed if tools for managing radiation damage in practical data collection are to be conveniently robust enough to be useful in real time.
PMCID: PMC3083914  PMID: 21525647
radiation damage; data collection; strategy; beamline software; datasets
18.  Molecular replacement then and now 
A brief overview, with examples, of the evolution of molecular-replacement methods and models over the past few years is presented.
The ‘phase problem’ in crystallography results from the inability to directly measure the phases of individual diffracted X-ray waves. While intensities are directly measured during data collection, phases must be obtained by other means. Several phasing methods are available (MIR, SAR, MAD, SAD and MR) and they all rely on the premise that phase information can be obtained if the positions of marker atoms in the unknown crystal structure are known. This paper is dedicated to the most popular phasing method, molecular replacement (MR), and represents a personal overview of the development, use and requirements of the methodology. The first description of noncrystallographic symmetry as a tool for structure determination was explained by Rossmann and Blow [Rossmann & Blow (1962 ▶), Acta Cryst. 15, 24–31]. The term ‘molecular replacement’ was introduced as the name of a book in which the early papers were collected and briefly reviewed [Rossmann (1972 ▶), The Molecular Replacement Method. New York: Gordon & Breach]. Several programs have evolved from the original concept to allow faster and more sophisticated searches, including six-dimensional searches and brute-force approaches. While careful selection of the resolution range for the search and the quality of the data will greatly influence the outcome, the correct choice of the search model is probably still the main criterion to guarantee success in solving a structure using MR. Two of the main parameters used to define the ‘best’ search model are sequence identity (25% or more) and structural similarity. Another parameter that may often be undervalued is the quality of the probe: there is clearly a relationship between the quality and the correctness of the chosen probe and its usefulness as a search model. Efforts should be made by all structural biologists to ensure that their deposited structures, which are potential search probes for future systems, are of the best possible quality.
PMCID: PMC3817701  PMID: 24189239
molecular replacement; models; accuracy; quality
19.  Crystal structure of lead(II) tartrate: a redetermination 
The redetermination of the crystal structure of lead tartrate from crystals grown in a gel medium confirmed the previous powder X-ray diffraction study in the space group P212121 with higher precision. Contradictions in the literature regarding space group and water content could be clarified.
Single crystals of poly[μ4-tartrato-κ6 O 1,O 3:O 1′:O 2,O 4:O 4′-lead], [Pb(C4H4O6)]n, were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ▶). Acta Cryst. C58, m596–m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb2+ cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb2+ cations. The resulting three-dimensional framework is stabilized by O—H⋯O hydrogen bonds between the OH groups of one tartrate anion and the carboxyl­ate O atoms of adjacent anions.
PMCID: PMC4331892
crystal structure; lead tartrate; gel growth; redetermination; O—H⋯O hydrogen bonds
20.  Anharmonicity and isomorphic phase transition: a multi-temperature X-ray single-crystal and powder diffraction study of 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole 
Iucrj  2014;1(Pt 2):110-118.
Multi-temperature single-crystal and powder diffraction experiments on 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole show that this crystal undergoes an isomorphic phase transition with the coexistence of two phase domains over a wide temperature range. The anharmonic approach was the only way to model the resulting disorder.
The harmonic model of atomic nuclear motions is usually enough for multipole modelling of high-resolution X-ray diffraction data; however, in some molecular crystals, such as 1-(2′-aminophenyl)-2-methyl-4-nitro-1H-imidazole [Paul, Kubicki, Jelsch et al. (2011 ▶). Acta Cryst. B67, 365–378], it may not be sufficient for a correct description of the charge-density distribution. Multipole refinement using harmonic atom vibrations does not lead to the best electron density model in this case and the so-called ‘shashlik-like’ pattern of positive and negative residual electron density peaks is observed in the vicinity of some atoms. This slight disorder, which cannot be modelled by split atoms, was solved using third-order anharmonic nuclear motion (ANM) parameters. Multipole refinement of the experimental high-resolution X-ray diffraction data of 1-(2′-aminophenyl)-2-methyl-4-nitro-1H-imidazole at three different temperatures (10, 35 and 70 K) and a series of powder diffraction experiments (20 ≤ T ≤ 300 K) were performed to relate this anharmonicity observed for several light atoms (N atoms of amino and nitro groups, and O atoms of nitro groups) to an isomorphic phase transition reflected by a change in the b cell parameter around 65 K. The observed disorder may result from the coexistence of domains of two phases over a large temperature range, as shown by low-temperature powder diffraction.
PMCID: PMC4062092  PMID: 25075327
anharmonicity; isomorphic phase transition; experimental charge density; X-ray closed-circuit helium cryostat; Hansen–Coppens model; multiple-temperature powder diffraction
21.  Corrigenda 
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].
PMCID: PMC3344282
22.  2-[(E)-(Dimethylamino)methylene­amino]-N-phenylbenzenesulfonamide. Corrigendum 
Corrigendum to Acta Cryst. (2007), E63, o4446.
Corrections are made to the name of the author and the address in Zhong [Acta Cryst. (2007), E63, o4446].
PMCID: PMC2914900  PMID: 21200447
23.  Poly[[diaqua­caesium(II)]bis­(μ3-3-carboxy­pyrazine-2-carboxyl­ato)]. Corrigendum 
Corrigendum to Acta Cryst. (2007), E63, m1783–m1784.
Corrections are made to the formulation and scheme in Tombul, Güven & Büyükgüngör [Acta Cryst. (2007) E63, m1783–m1784].
PMCID: PMC2960761  PMID: 21201833
24.  Investigation of depth-resolved nanoscale structural changes in regulated cell proliferation and chromatin decondensation: erratum 
Biomedical Optics Express  2013;4(11):2491.
We correct minor errors in two equations reported in our paper [Biomed. Opt. Express 4, 596–613 (2013)]; an additional factor of two was mistakenly incorporated in Eqs. (3) and (4). We give the correct equations below. All the simulations and experiments in the previous paper were performed using the correct equations, and therefore, remain the same.
PMCID: PMC3829542  PMID: 24312743
(180.3170) Interference microscopy; (300.6300) Spectroscopy, Fourier transforms; (170.4730) Optical pathology; (170.1610) Clinical applications
25.  catena-Poly[[(2,9-dimethyl-1,10-phenanthroline-κ2 N,N′)lead(II)]-di-μ-2-hydroxy­benzoato-κ3 O 1,O 1′:O 2;κ3 O 2:O 1,O 1′]. Corrigendum 
Corrigendum to Acta Cryst. (2007), E63, m2678.
A reference in the paper by Xuan & Zhao [Acta Cryst. (2007), E63, m2678] is replaced.
PMCID: PMC2914878  PMID: 21200450

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