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MolProbity: all-atom structure validation for macromolecular crystallography.

Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC - Acta Crystallogr. D Biol. Crystallogr. (2009)

Bottom Line: However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers.It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures.MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, Duke University, Durham, NC 27710, USA.

ABSTRACT
MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

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Close-up of a ribose-pucker outlier in the multi-criterion kinemage for 1n78, with backbone and bases turned on. C574 has a short phosphate-to-glycosidic bond perpendicular (magenta line and cross), but was fitted with an intermediate pucker near C3′-endo. The bad pucker torques the connected groups strongly, probably causing the bond-angle outliers (red) and steric clashes (hot-pink spikes). Note that C574 is in the binding interface between RNA (white backbone) and enzyme (yellow backbone) close to the active site.
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fig6: Close-up of a ribose-pucker outlier in the multi-criterion kinemage for 1n78, with backbone and bases turned on. C574 has a short phosphate-to-glycosidic bond perpendicular (magenta line and cross), but was fitted with an intermediate pucker near C3′-endo. The bad pucker torques the connected groups strongly, probably causing the bond-angle outliers (red) and steric clashes (hot-pink spikes). Note that C574 is in the binding interface between RNA (white backbone) and enzyme (yellow backbone) close to the active site.

Mentions: In addition, MolProbity now includes diagnosis of suspect ribose puckers and torsion-angle analysis of preferred RNA backbone conformers. We have found that the dominant C3′-­endo and C2′-endo sugar puckers are highly correlated to the perpendicular distance between the C1′–N1/9 glycosidic bond vector and the following (3′) phosphate: >2.9 Å for C3′-­endo and <2.9 Å for C2′-endo. MolProbity checks this distance against the modeled sugar pucker, as well as outliers in individual ∊ or δ values. All such outliers are listed in the multi-chart and ribose-pucker outliers are flagged in the kinemage (Fig. 1 ▶). An example is shown in Fig. 6 ▶, where what should have been a C2′-endo pucker (by the short perpendicular) was fitted as an intermediate unfavorable pucker close to the more common default C3′-endo pucker, also producing geometry and ∊ outliers.


MolProbity: all-atom structure validation for macromolecular crystallography.

Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC - Acta Crystallogr. D Biol. Crystallogr. (2009)

Close-up of a ribose-pucker outlier in the multi-criterion kinemage for 1n78, with backbone and bases turned on. C574 has a short phosphate-to-glycosidic bond perpendicular (magenta line and cross), but was fitted with an intermediate pucker near C3′-endo. The bad pucker torques the connected groups strongly, probably causing the bond-angle outliers (red) and steric clashes (hot-pink spikes). Note that C574 is in the binding interface between RNA (white backbone) and enzyme (yellow backbone) close to the active site.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2803126&req=5

fig6: Close-up of a ribose-pucker outlier in the multi-criterion kinemage for 1n78, with backbone and bases turned on. C574 has a short phosphate-to-glycosidic bond perpendicular (magenta line and cross), but was fitted with an intermediate pucker near C3′-endo. The bad pucker torques the connected groups strongly, probably causing the bond-angle outliers (red) and steric clashes (hot-pink spikes). Note that C574 is in the binding interface between RNA (white backbone) and enzyme (yellow backbone) close to the active site.
Mentions: In addition, MolProbity now includes diagnosis of suspect ribose puckers and torsion-angle analysis of preferred RNA backbone conformers. We have found that the dominant C3′-­endo and C2′-endo sugar puckers are highly correlated to the perpendicular distance between the C1′–N1/9 glycosidic bond vector and the following (3′) phosphate: >2.9 Å for C3′-­endo and <2.9 Å for C2′-endo. MolProbity checks this distance against the modeled sugar pucker, as well as outliers in individual ∊ or δ values. All such outliers are listed in the multi-chart and ribose-pucker outliers are flagged in the kinemage (Fig. 1 ▶). An example is shown in Fig. 6 ▶, where what should have been a C2′-endo pucker (by the short perpendicular) was fitted as an intermediate unfavorable pucker close to the more common default C3′-endo pucker, also producing geometry and ∊ outliers.

Bottom Line: However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers.It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures.MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry, Duke University, Durham, NC 27710, USA.

ABSTRACT
MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.

Show MeSH