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Surprises and pitfalls arising from (pseudo)symmetry.

Zwart PH, Grosse-Kunstleve RW, Lebedev AA, Murshudov GN, Adams PD - Acta Crystallogr. D Biol. Crystallogr. (2007)

Bottom Line: When more than a single molecule is present in the asymmetric unit, various pathological situations such as twinning, modulated crystals and pseudo translational or rotational symmetry can arise.The presence of pseudosymmetry can lead to uncertainties about the correct space group, especially in the presence of twinning.The main concepts are illustrated with several examples from the literature and the Protein Data Bank.

View Article: PubMed Central - HTML - PubMed

Affiliation: Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, One Cyclotron Road, Building 6R2100, Berkeley, CA 94720, USA. phzwart@lbl.gov

ABSTRACT
It is not uncommon for protein crystals to crystallize with more than a single molecule per asymmetric unit. When more than a single molecule is present in the asymmetric unit, various pathological situations such as twinning, modulated crystals and pseudo translational or rotational symmetry can arise. The presence of pseudosymmetry can lead to uncertainties about the correct space group, especially in the presence of twinning. The background to certain common pathologies is presented and a new notation for space groups in unusual settings is introduced. The main concepts are illustrated with several examples from the literature and the Protein Data Bank.

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A graphical representation of all group–subgroup relations for P222 and it subgroups. The arrows connecting two space groups represent the addition of a single operator to the parent space groups and its result.
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fig2: A graphical representation of all group–subgroup relations for P222 and it subgroups. The arrows connecting two space groups represent the addition of a single operator to the parent space groups and its result.

Mentions: Note that if the operators of P211 are combined with one of the ‘remaining’ operators (−x, y, −z) or (−x, −y, z), the other operator is generated by group multiplication, leading to P222. A depiction of the relations between all subgroups of P222 is shown in Fig. 2 ▶. In this figure, nodes representing space groups are linked with arrows. The arrows between the space groups indicate that the multiplication of a single symmetry operator into a group results in the other group. For example, the arrow in Fig. 2 ▶ from P1 to P211 indicates that a single symmetry element [in this case (x, −y, −z)] combined with P1 results in the space group P211.


Surprises and pitfalls arising from (pseudo)symmetry.

Zwart PH, Grosse-Kunstleve RW, Lebedev AA, Murshudov GN, Adams PD - Acta Crystallogr. D Biol. Crystallogr. (2007)

A graphical representation of all group–subgroup relations for P222 and it subgroups. The arrows connecting two space groups represent the addition of a single operator to the parent space groups and its result.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2394827&req=5

fig2: A graphical representation of all group–subgroup relations for P222 and it subgroups. The arrows connecting two space groups represent the addition of a single operator to the parent space groups and its result.
Mentions: Note that if the operators of P211 are combined with one of the ‘remaining’ operators (−x, y, −z) or (−x, −y, z), the other operator is generated by group multiplication, leading to P222. A depiction of the relations between all subgroups of P222 is shown in Fig. 2 ▶. In this figure, nodes representing space groups are linked with arrows. The arrows between the space groups indicate that the multiplication of a single symmetry operator into a group results in the other group. For example, the arrow in Fig. 2 ▶ from P1 to P211 indicates that a single symmetry element [in this case (x, −y, −z)] combined with P1 results in the space group P211.

Bottom Line: When more than a single molecule is present in the asymmetric unit, various pathological situations such as twinning, modulated crystals and pseudo translational or rotational symmetry can arise.The presence of pseudosymmetry can lead to uncertainties about the correct space group, especially in the presence of twinning.The main concepts are illustrated with several examples from the literature and the Protein Data Bank.

View Article: PubMed Central - HTML - PubMed

Affiliation: Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, One Cyclotron Road, Building 6R2100, Berkeley, CA 94720, USA. phzwart@lbl.gov

ABSTRACT
It is not uncommon for protein crystals to crystallize with more than a single molecule per asymmetric unit. When more than a single molecule is present in the asymmetric unit, various pathological situations such as twinning, modulated crystals and pseudo translational or rotational symmetry can arise. The presence of pseudosymmetry can lead to uncertainties about the correct space group, especially in the presence of twinning. The background to certain common pathologies is presented and a new notation for space groups in unusual settings is introduced. The main concepts are illustrated with several examples from the literature and the Protein Data Bank.

Show MeSH
Related in: MedlinePlus