Ten years of probabilistic estimates of biocrystal solvent content: new insightsvianonparametric kernel density estimate

Abstract

The probabilistic estimate of the solvent content (Matthews probability) was first introduced in 2003. Given that the Matthews probability is based on prior information, revisiting the empirical foundation of this widely used solvent-content estimate is appropriate. The parameter set for the original Matthews probability distribution function employed in MATTPROB has been updated after ten years of rapid PDB growth. A new nonparametric kernel density estimator has been implemented to calculate the Matthews probabilities directly from empirical solvent-content data, thus avoiding the need to revise the multiple parameters of the original binned empirical fit function. The influence and dependency of other possible parameters determining the solvent content of protein crystals have been examined. Detailed analysis showed that resolution is the primary and dominating model parameter correlated with solvent content. Modifications of protein specific density for low molecular weight have no practical effect, and there is no correlation with oligomerization state. A weak, and in practice irrelevant, dependency on symmetry and molecular weight is present, but cannot be satisfactorily explained by simple linear or categorical models. The Bayesian argument that the observed resolution represents only a lower limit for the true diffraction potential of the crystal is maintained. The new kernel density estimator is implemented as the primary option in the MATTPROB web application at http://www.ruppweb.org/mattprob/.

Structural Basis of Ribosomal S6 Kinase 1 (RSK1) Inhibition by S100B Protein

“…Data were processed with XDS. Matthews probability calculations indicate the highest probability of an asymmetric complex forming between a single dimer of S100B and a single RSK1 peptide in all crystal forms (20). This was later confirmed after the phase problem was solved by molecular replacement in PHASER with a high resolution structure of S100B as a searching model (21)(22)(23).…”

“…In the autoinhibited MAPK-bound state residues between 690 and 707 form the ␣L helix, and the C-terminal tail from 712 is involved in MAPK binding (13). B, Matthews probabilities of crystal structure A calculated for apo-S100B and for 2:1 and 2:2 complexes (20). In all determined structures the 2:1 complex was the most preferred content.…”

Identification and Crystallographic Analysis of a New Carbohydrate Acetylesterase (SmAcE1) from Sinorhizobium meliloti

“…The presence of hexameric SmAcE1 in an asymmetric unit gives a calculated Matthews coefficient V M of 3.58 Å 3 Da −1 , which corresponds to a solvent content of 65.65%. The V M is within a range frequently observed in protein crystals [36][37][38]. For structural studies, we used molecular replacement (MR) method and the program Phaser [40] to search for the structure solution.…”

The Use of Connected Masks for Reconstructing the Single Particle Image from X-Ray Diffraction Data. III. Maximum-Likelihood Based Strategies to Select Solution of the Phase Problem

“…В данной работе мы характеризуем предполагаемый размер области либо количеством точек в маске, либо удельным объемом, определяемым как отношение объема области (в кубических ангстремах) к молекулярной массе частицы (в дальтонах). В кристаллографии при оценке процентного содержания растворителя в элементарной ячейке принято считать удельный объем области молекулы равным 1.23 Å 3 /Da [45,46]. Однако эта оценка не является оптимальной при работе в зоне низкого разрешения, когда границы молекулы существенно сглажены.…”