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Solvents

Solvents

A solvent is a substance, most often a liquid, that can dissolve other substances. Here, the substance being dissolved is called a solute. When a solvent and a solute combine, they form a solution - a homogenous mixture of both the solvent and the solute. Water is a universal biological solvent. Its polar structure allows it to dissolve many other polar compounds. The ability of water to dissolve is governed by a balance between water molecules binding to each other and binding to the solute.
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Capturing Flow-weighted Water and Suspended Particulates from Agricultural Canals During Drainage Events

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Polder maps: improving OMIT maps by excluding bulk solvent.

Dorothee Liebschner¹, Pavel V Afonine¹, Nigel W Moriarty¹

¹Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA.

Acta Crystallographica. Section D, Structural Biology

|February 9, 2017

Summary

This summary is machine-generated.

OMIT maps in crystallography are often biased by existing models. Polder OMIT maps improve validation by excluding bulk solvent, enhancing the detection of weak electron densities for ligands and other structures.

Keywords:

OMIT maps PHENIX bulk solvent ligand validation polder maps residual (difference) Fourier synthesis weak density

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Area of Science:

Crystallography
Structural Biology
Biochemistry

Background:

Crystallographic maps used in structure solution and validation are typically model-biased due to the incorporation of model information during their calculation.
This inherent bias poses a challenge for accurately validating atomic models, as any additions to the model can artificially appear in the maps.
OMIT maps are employed to verify atom presence, but conventional methods are complicated by the ubiquitous bulk-solvent model, which can obscure weak electron densities.

Purpose of the Study:

To address the limitations of standard OMIT maps in crystallographic model validation.
To introduce and describe the utility of polder OMIT maps for improved detection of weak electron densities.
To present tools for generating polder OMIT maps within the PHENIX software suite.

Main Methods:

Calculation of OMIT maps by excluding specific atoms from the structural model and recomputing structure factors.
Modification of the OMIT map calculation to exclude bulk solvent from selected regions, creating polder OMIT maps.
Implementation and availability of these polder OMIT map tools within the PHENIX crystallography software.

Main Results:

Polder OMIT maps demonstrate enhanced interpretative power compared to standard OMIT maps.
These maps effectively reveal weak electron densities that are often obscured by the bulk-solvent model.
The utility of polder OMIT maps is shown for identifying ligands, solvent molecules, side chains, and residues in challenging structural regions.

Conclusions:

Polder OMIT maps offer a significant improvement for crystallographic model validation by mitigating bulk-solvent effects.
This method is particularly valuable for visualizing low-electron-density features, aiding in the accurate interpretation of crystal structures.
The availability of these tools in PHENIX facilitates their application in routine structural biology workflows.