1,720,993 research outputs found
mrtailor: a tool for PDB-file preparation for the generation of external restraints
No full textModel building starting from, for example, a molecular-replacement solution with low sequence similarity introduces model bias, which can be difficult to detect, especially at low resolution. The program mrtailor removes low-similarity regions from a template PDB file according to sequence similarity between the target sequence and the template sequence and maps the target sequence onto the PDB file. The modified PDB file can be used to generate external restraints for low-resolution refinement with reduced model bias and can be used as a starting point for model building and refinement. The program can call ProSMART [Nicholls et al. (2012), Acta Cryst. D68, 404-417] directly in order to create external restraints suitable for REFMAC5 [Murshudov et al. (2011), Acta Cryst. D67, 355-367]. Both a command-line version and a GUI exist.Volkswagen Stiftung via the Niedersachsen-professu
New method to compute R-complete enables maximum likelihood refinement for small datasets
No full textThe crystallographic reliability index R-complete is based on a method proposed more than two decades ago. Because its calculation is computationally expensive its use did not spread into the crystallographic community in favor of the cross-validation method known as R-free. The importance of R-free has grown beyond a pure validation tool. However, its application requires a sufficiently large dataset. In this work we assess the reliability of R-complete and we compare it with k-fold cross-validation, bootstrapping, and jackknifing. As opposed to proper cross-validation as realized with R-free, R-complete relies on a method of reducing bias from the structural model. We compare two different methods reducing model bias and question the widely spread notion that random parameter shifts are required for this purpose. We show that R-complete has as little statistical bias as R-free with the benefit of a much smaller variance. Because the calculation of R-complete is based on the entire dataset instead of a small subset, it allows the estimation of maximum likelihood parameters even for small datasets. R-complete enables maximum likelihood-based refinement to be extended to virtually all areas of crystallographic structure determination including high-pressure studies, neutron diffraction studies, and datasets from free electron lasers.Volkswagen Stiftung via the Niedersachsenprofessu
Geometric properties of nucleic acids with potential for autobuilding
No full textMedium- to high-resolution X-ray structures of DNA and RNA molecules were investigated to find geometric properties useful for automated model building in crystallographic electron-density maps. We describe a simple method, starting from a list of electron-density 'blobs', for identifying backbone phosphates and nucleic acid bases based on properties of the local electron-density distribution. This knowledge should be useful for the automated building of nucleic acid models into electron-density maps. We show that the distances and angles involving C1' and the P atoms, using the pseudo-torsion angles eta' and theta' that describe the ... P-C1'-P-C1' ... chain, provide a promising basis for building the nucleic acid polymer. These quantities show reasonably narrow distributions with asymmetry that should allow the direction of the phosphate backbone to be established
A magic triangle for experimental phasing of macromolecules
No full textObtaining phase information for the solution of macromolecular structures is still one of the bottlenecks in X-ray crystallography. 5-Amino-2,4,6-triiodoisophthalic acid (I3C), in which three covalently bound iodines form an equilateral triangle, was incorporated into proteins in order to obtain phases by singlewavelength anomalous dispersion (SAD). An improved binding capability compared with simple heavy-metal ions, ready availability, improved recognition of potential heavy-atom sites and low toxicity make I3C particularly suitable for experimental phasing
Refinement of macromolecular structures against neutron data with SHELXL2013
No full textSome of the improvements in SHELX2013 make SHELXL convenient to use for refinement of macromolecular structures against neutron data without the support of X-ray data. The new NEUT instruction adjusts the behaviour of the SFAC instruction as well as the default bond lengths of the AFIX instructions. This work presents a protocol on how to use SHELXL for refinement of protein structures against neutron data. It includes restraints extending the Engh & Huber [Acta Cryst. (1991), A47, 392-400] restraints to H atoms and discusses several of the features of SHELXL that make the program particularly useful for the investigation of H atoms with neutron diffraction. SHELXL2013 is already adequate for the refinement of small molecules against neutron data, but there is still room for improvement, like the introduction of chain IDs for the refinement of macromolecular structures
The structure of tripeptidyl peptidase I (TPP1) provides insight into the molecular basis of late infantile neuronal ceroid lipofuscinosis
No full textThe magic triangle goes MAD: experimental phasing with a bromine derivative
No full textExperimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional groups for binding to proteins. The phasing tool 5-amino-2,4,6-tribromoisophthalic acid (B3C) contains three functional groups (two carboxylate groups and one amino group) that interact with proteins via hydrogen bonds. Three Br atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus readily identified in the heavy-atom substructure. B3C was incorpo-rated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br K edge was success-fully carried out. Radiation damage to the bromine–carbon bond was investigated. A comparison with the phasing tool I3C that contains three I atoms for single-wavelength anomalous dispersion (SAD) phasing was also carried out
Structures of viscotoxins A1 and B2 from European mistletoe solved using native data alone
No full textCrystals of the cytotoxic thionin proteins viscotoxins A1 and B2 extracted from mistletoe diffracted to high resolution (1.25 and 1.05 angstrom, respectively) and are excellent candidates for testing crystallographic methods. Ab initio direct methods were only successful in solving the viscotoxin B2 structure, which with 861 unique non-H atoms is one of the largest unknown structures without an atom heavier than sulfur to be solved in this way, but sulfur-SAD phasing provided a convincing solution for viscotoxin A1. Both proteins form dimers in the crystal and viscotoxin B2 (net charge +4 per monomer), but not viscotoxin A1 (net charge +6), is coordinated by sulfate or phosphate anions. The viscotoxin A1 crystal has a higher solvent content than the viscotoxin B2 crystal (49% as opposed to 28%) with solvent channels along the crystallographic 43 axes
Structure of Hormaomycin, a Naturally Occurring Cyclic Octadepsipeptide, in the Crystal
No full textThe structure of hormaomycin has been determined in two crystals grown under different conditions, i. e. in the absence and in the presence of magnesium chloride. In both crystals, the macrocyclic hexadepsipeptide assumes a rather flat conformation, and the dipeptide side chain resides in the same equatorial plane. This is a significant difference in comparison with the compact bent conformation of hormaomycin in solution, as previously determined by an extensive NMR study
- …
