More space-group changes

Marsh, Richard E.; Bernal, Ivan

doi:10.1107/s0108768187009492

Cited by 60 publications

(35 citation statements)

References 7 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As was pointed out for small molecules (Mighell et al 1983; Baur and Kassner 1992; Herbstein and Marsh 1998; Marsh 2002; Marsh and Spek 2001; Marsh et al 2002), many structures are reported in the wrong symmetry, and in most cases, this wrong symmetry is unnecessarily low (Baur and Tillmanns 1986). In general, there are two types of mistakes in choosing space groups: incorrect space group and correct system or both incorrect space group and system (Marsh 1995; Marsh and Bernal 1995).…”

Section: Discussionmentioning

confidence: 99%

Analysis of solvent content and oligomeric states in protein crystals—does symmetry matter?

et al. 2008

View full text Add to dashboard Cite

A nonredundant set of 9081 protein crystal structures in the Protein Data Bank was used to examine the solvent content, the number of polypeptide chains, and the oligomeric states of proteins in crystals as a function of crystal symmetry (as classified by crystal systems and space groups). It was found that there is a correlation between solvent content and crystal symmetry. Surprisingly, proteins crystallizing in lower symmetry systems have lower solvent content compared to those crystallizing in higher symmetry systems. Nevertheless, there is no universal correlation between solvent content and preferences of macromolecules to crystallize in certain space groups. Crystal symmetry as a function of oligomeric state was examined, where trimers, tetramers, and hexamers were found to prefer to crystallize in systems where the oligomer symmetry could be incorporated in the crystal symmetry. Our analysis also shows that the frequency distribution within the enantiomorphous pairs of space groups does not differ significantly, in contrast to previous reports.Keywords: solvent content; Matthews coefficient; protein crystals; oligomerization; space group frequency Supplemental material: see www.proteinscience.orgWater plays an important role in the structure of biomolecules and often influences protein function. Water molecules not only affect protein folding, but also mediate biological processes such as enzymatic reactions and molecular recognition. Information about the fraction of water (solvent) plays a significant role in the X-ray structure determination process. First, knowledge of the solvent content helps to determine the number of molecules in the asymmetric unit (Matthews 1968), which is crucial in early stages of crystal structure determination. Second, an approximate value of solvent content is needed for significant phase improvement by solvent flattening methods (Wang 1985;Leslie 1987;Abrahams and Leslie 1996), which is necessary to resolve the inherent phase ambiguity in single anomalous diffraction (SAD) experiments. For both SAD and MAD (multiwavelength anomalous diffraction) (Hendrickson 1991;Hendrickson et al. 1990), phase improvement by solvent flattening is critical for low resolution data (Kirillova et al. 2007), especially when non-crystallographic symmetry cannot be applied.Matthews (1968) observed that the solvent content in protein crystals ranged from 27% to 65%, with an average of 43%. He also showed that the quantity V M (the Matthews coefficient, defined as the ratio of the volume of the asymmetric unit to the molecular weight of all

show abstract

Section: Discussionmentioning

confidence: 99%

Analysis of solvent content and oligomeric states in protein crystals—does symmetry matter?

et al. 2008

View full text Add to dashboard Cite

show abstract

“…To be more precise, by using the generalized coordinate for polyhedral interconversion pathways, [25] we can estimate that structure [ 22] Center: coordination sphere of a ten-coordinated Sm atom [23] with the shape of a sphenocorona. Right: trigonal bipyramidal arrangement of the five carbonato ligands around the Ce atom in the guanidinium salt [24] of…”

Section: Five Bidentate Ligandsmentioning

confidence: 99%

Stereochemistry of Compounds with Coordination Number Ten

Ruiz‐Martínez

Álvarez

2009

Chemistry A European J

114

115

View full text Add to dashboard Cite

The stereochemistry of ten-coordinate rare-earth and transition-metal compounds is studied from the point of view of continuous shape measures (CShM) and derived tools. A total of 19 ideal ten-vertex polyhedra belonging to 12 different symmetry point groups have been considered, from which nine are retained for the description of the stereochemistries of all studied compounds. The structures of the coordination spheres are analyzed by families, according to the denticity and topology of the ligands. Some ligand topologies are seen to consistently favor usually neglected ideal polyhedra, such as the capped trigonal cupola.

show abstract

“…The results were compared with the results from the ADDSYM routine of PLATON and with space-group reinterpretations noted in the CSD. A comparison with space-group corrections tabulated in the literature (Marsh & Herbstein, 1988;Kapon & Reisner, 1990;Marsh, 1994aMarsh, , b, 1995Marsh, , 1997Marsh, , 1999Marsh, , 2002Marsh, , 2004Marsh, , 2005Marsh, , 2009Marsh & Bernal, 1995;Herbstein & Marsh, 1998;Marsh & Spek, 2001;Marsh et al, 2002;Clemente, 2003;Marsh & Clemente, 2007) showed that the overlap between our list and the published lists is very small, because most of the structures corrected in those papers either included metal atoms, were enantiopure, or were originally in non-Sohnke space groups like Cc.…”

Section: Examination Of Conformational Similarity and Of Pseudosymmetrymentioning

confidence: 93%

A list of organic kryptoracemates

Fábián

Brock

2010

Acta Crystallogr Sect B

View full text Add to dashboard Cite

A list of 181 organic kryptoracemates has been compiled. This class of crystallographic oddities is made up of racemic compounds (i.e. pairs of resolvable enantiomers) that happen to crystallize in Sohnke space groups (i.e. groups that include only proper symmetry operations). Most (151) of the 181 structures could have crystallized as ordered structures in non-Sohnke groups. The remaining 30 structures do not fully meet this criterion but would have been classified as kryptoracemates by previous authors. Examples were found and checked with the aid of available software for searching the Cambridge Structural Database, for generating and comparing InChI strings, and for validating crystal structures. The pairs of enantiomers in the true kryptoracemates usually have very similar conformations; often the match is near-perfect. There is a pseudosymmetric relationship of the enantiomers in about 60% of the kryptoracemate structures, but the deviations from inversion or glide symmetry are usually quite easy to spot. Kryptoracemates were found to account for 0.1% of all organic structures containing either a racemic compound, a meso molecule, or some other achiral molecule. The centroid of a pair of enantiomers is more likely (99.9% versus 99% probability) to be located on an inversion center than is the centroid of a potentially centrosymmetric molecule.

show abstract

More space-group changes

Cited by 60 publications

References 7 publications

Analysis of solvent content and oligomeric states in protein crystals—does symmetry matter?

Analysis of solvent content and oligomeric states in protein crystals—does symmetry matter?

Stereochemistry of Compounds with Coordination Number Ten

A list of organic kryptoracemates

Contact Info

Product

Resources

About