Limits...
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.

Show MeSH
Two multi-criterion validation kinemages illustrating the successful outcome of an overall process of MolProbity diagnosis and structure improvement. (a) The original 1lpl Cap-Gly structure (Li et al., 2002 ▶) shows three major clusters of clash, rotamer and Ramachandran problems plus a few isolated outliers. (b) The corrected 1tov structure (Arendall et al., 2005 ▶) has essentially no outliers, a 4% lower R                  free, a bound sulfate and an additional turn of helix at the N-terminus.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2803126&req=5

fig2: Two multi-criterion validation kinemages illustrating the successful outcome of an overall process of MolProbity diagnosis and structure improvement. (a) The original 1lpl Cap-Gly structure (Li et al., 2002 ▶) shows three major clusters of clash, rotamer and Ramachandran problems plus a few isolated outliers. (b) The corrected 1tov structure (Arendall et al., 2005 ▶) has essentially no outliers, a 4% lower R free, a bound sulfate and an additional turn of helix at the N-terminus.

Mentions: The crucial final step in the MolProbity process is for the crystallographer to download the result files and work off-line to correct as many of the diagnosed problems as feasible. Rebuilding with consideration of the validation outliers, the electron density and the surrounding model is usually per­formed either in Coot (Emsley & Cowtan, 2004 ▶) or in KiNG (Chen et al., 2009 ▶). At resolutions of about 2.5 Å or better it is possible to correct the great majority of outliers (Arendall et al., 2005 ▶), with an order-of-magnitude improvement in the various MolProbity scores and some improvement in geometry, map quality, R factor and R free. An example is shown in Fig. 2 ▶ with before-and-after multi-criterion kinemages.


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)

Two multi-criterion validation kinemages illustrating the successful outcome of an overall process of MolProbity diagnosis and structure improvement. (a) The original 1lpl Cap-Gly structure (Li et al., 2002 ▶) shows three major clusters of clash, rotamer and Ramachandran problems plus a few isolated outliers. (b) The corrected 1tov structure (Arendall et al., 2005 ▶) has essentially no outliers, a 4% lower R                  free, a bound sulfate and an additional turn of helix at the N-terminus.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig2: Two multi-criterion validation kinemages illustrating the successful outcome of an overall process of MolProbity diagnosis and structure improvement. (a) The original 1lpl Cap-Gly structure (Li et al., 2002 ▶) shows three major clusters of clash, rotamer and Ramachandran problems plus a few isolated outliers. (b) The corrected 1tov structure (Arendall et al., 2005 ▶) has essentially no outliers, a 4% lower R free, a bound sulfate and an additional turn of helix at the N-terminus.
Mentions: The crucial final step in the MolProbity process is for the crystallographer to download the result files and work off-line to correct as many of the diagnosed problems as feasible. Rebuilding with consideration of the validation outliers, the electron density and the surrounding model is usually per­formed either in Coot (Emsley & Cowtan, 2004 ▶) or in KiNG (Chen et al., 2009 ▶). At resolutions of about 2.5 Å or better it is possible to correct the great majority of outliers (Arendall et al., 2005 ▶), with an order-of-magnitude improvement in the various MolProbity scores and some improvement in geometry, map quality, R factor and R free. An example is shown in Fig. 2 ▶ with before-and-after multi-criterion kinemages.

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