scholarly journals Critical evaluation of a crystal structure of nitrogenase with bound N2 ligands

2021 ◽  
Author(s):  
Justin Bergmann ◽  
Esko Oksanen ◽  
Ulf Ryde
Keyword(s):  
Electron Density ◽  
Resting State ◽  
Critical Evaluation ◽  
Real Space ◽  
Convincing Evidence ◽  
Crystallographic Structure ◽  
Raw Data ◽  
Density Maps ◽  
Sulfide Ligands ◽  
Sulfide Ions

AbstractRecently, a 1.83 Å crystallographic structure of nitrogenase was suggested to show N2-derived ligands at three sites in the catalytic FeMo cluster, replacing the three $$\mu_{2}$$ μ 2 bridging sulfide ligands (two in one subunit and the third in the other subunit) (Kang et al. in Science 368: 1381–1385, 2020). Naturally, such a structure is sensational, having strong bearings on the reaction mechanism of the enzyme. Therefore, it is highly important to ensure that the interpretation of the structure is correct. Here, we use standard crystallographic refinement and quantum refinement to evaluate the structure. We show that the original crystallographic raw data are strongly anisotropic, with a much lower resolution in certain directions than others. This, together with the questionable use of anisotropic B factors, give atoms an elongated shape, which may look like diatomic atoms. In terms of standard electron-density maps and real-space Z scores, a resting-state structure with no dissociated sulfide ligands fits the raw data better than the interpretation suggested by the crystallographers. The anomalous electron density at 7100 eV is weaker for the putative N2 ligands, but not lower than for several of the $${\mu }_{3}$$ μ 3 bridging sulfide ions and not lower than what can be expected from a statistical analysis of the densities. Therefore, we find no convincing evidence for any N2 binding to the FeMo cluster. Instead, a standard resting state without any dissociated ligands seems to be the most likely interpretation of the structure. Likewise, we find no support that the homocitrate ligand should show monodentate binding. Graphic abstract

scholarly journals Statistical quality indicators for electron-density maps

2012 ◽  
Vol 68 (4) ◽  
pp. 454-467 ◽  
Author(s):  
Ian J. Tickle
Keyword(s):  
Electron Density ◽  
Statistical Significance ◽  
Significance Test ◽  
Real Space ◽  
Structure Model ◽  
Space Correlation ◽  
The Real ◽  
Difference Density ◽  
Density Maps ◽  
The Difference

The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all validation techniques is to verify the accuracy of the model, since precision is an inherent property of the crystal and the data. It is demonstrated that the principal weakness of both of the above metrics is their inability to distinguish the accuracy of the model from its precision. Furthermore, neither of these metrics in their usual implementation indicate the statistical significance of the result. The statistical properties of electron-density maps are reviewed and an improved alternative likelihood-based metric is suggested. This leads naturally to a χ2 significance test of the difference density using the real-space difference density Z score (RSZD). This is a metric purely of the local model accuracy, as required for effective model validation and structure optimization by practising crystallographers prior to submission of a structure model to the PDB. A new real-space observed density Z score (RSZO) is also proposed; this is a metric purely of the model precision, as a substitute for other precision metrics such as the B factor.

scholarly journals XGen: Real-Space Fitting of Complex Ligand Conformational Ensembles to X-ray Electron Density Maps

2020 ◽  
Vol 63 (18) ◽  
pp. 10509-10528
Author(s):  
Ajay N. Jain ◽  
Ann E. Cleves ◽  
Alexander C. Brueckner ◽  
Charles A. Lesburg ◽  
Qiaolin Deng ◽  
...  
Keyword(s):  
Electron Density ◽  
Real Space ◽  
X Ray ◽  
Conformational Ensembles ◽  
Density Maps ◽  
Complex Ligand

scholarly journals RNA Structure Refinement using the ERRASER-Phenix pipeline

2013 ◽  
Author(s):  
Fang-Chieh Chou ◽  
Nathaniel Echols ◽  
Thomas C. Terwilliger ◽  
Rhiju Das
Keyword(s):  
Electron Density ◽  
Rna Structure ◽  
Structure Refinement ◽  
Realistic Model ◽  
Real Space ◽  
Geometrical Quality ◽  
Density Maps ◽  
On Line ◽  
Rna Crystallography ◽  
Backbone Atoms

The final step of RNA crystallography involves the fitting of coordinates into electron density maps. The large number of backbone atoms in RNA presents a difficult and tedious challenge, particularly when experimental density is poor. The ERRASER-Phenix pipeline can improve an initial set of RNA coordinates automatically based on a physically realistic model of atomic-level RNA interactions. The pipeline couples diffraction-based refinement in Phenix with the Rosetta-based real-space refinement protocol ERRASER (Enumerative Real-Space Refinement ASsisted by Electron density under Rosetta). The combination of ERRASER and Phenix can improve the geometrical quality of RNA crystallographic models while maintaining or improving the fit to the diffraction data (as measured by Rfree). Here we present a complete tutorial for running ERRASER-Phenix through the Phenix GUI, from the command-line, and via an application in the Rosetta On-line Server that Includes Everyone (ROSIE).

scholarly journals Automated nucleic acid chain tracing in real time

IUCrJ ◽  
2014 ◽  
Vol 1 (6) ◽  
pp. 387-392 ◽  
Author(s):  
Kevin Cowtan
Keyword(s):  
Electron Density ◽  
Model Building ◽  
Protein Structures ◽  
Current View ◽  
Crystallographic Structure ◽  
Large Structures ◽  
Density Maps ◽  
Structure Solution ◽  
Automated Model Building ◽  
Electron Density Map

The crystallographic structure solution of nucleotides and nucleotide complexes is now commonplace. The resulting electron-density maps are often poorer than for proteins, and as a result interpretation in terms of an atomic model can require significant effort, particularly in the case of large structures. While model building can be performed automatically, as with proteins, the process is time-consuming, taking minutes to days depending on the software and the size of the structure. A method is presented for the automatic building of nucleotide chains into electron density which is fast enough to be used in interactive model-building software, with extended chain fragments built around the current view position in a fraction of a second. The speed of the method arises from the determination of the `fingerprint' of the sugar and phosphate groups in terms of conserved high-density and low-density features, coupled with a highly efficient scoring algorithm. Use cases include the rapid evaluation of an initial electron-density map, addition of nucleotide fragments to prebuilt protein structures, and in favourable cases the completion of the structure while automated model-building software is still running. The method has been incorporated into theCootsoftware package.

scholarly journals Determining crystal structures through crowdsourcing and coursework

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Scott Horowitz ◽  
◽  
Brian Koepnick ◽  
Raoul Martin ◽  
Agnes Tymieniecki ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Electron Density ◽  
Undergraduate Students ◽  
Model Building ◽  
Computer Game ◽  
Real Space ◽  
Amyloid Toxicity ◽  
New Family ◽  
Density Maps ◽  
New Feature

Abstract We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

scholarly journals Evaluation of macromolecular electron-density map quality using the correlation of local r.m.s. density

1999 ◽  
Vol 55 (11) ◽  
pp. 1872-1877 ◽  
Author(s):  
Thomas C. Terwilliger ◽  
Joel Berendzen
Keyword(s):  
Standard Deviation ◽  
Ab Initio ◽  
Electron Density ◽  
Heavy Atom ◽  
Real Space ◽  
Acta Cryst ◽  
Density Maps ◽  
Density Map ◽  
Electron Density Map ◽  
Trial Phase

It has recently been shown that the standard deviation of local r.m.s. electron density is a good indicator of the presence of distinct regions of solvent and protein in macromolecular electron-density maps [Terwilliger & Berendzen (1999). Acta Cryst. D55, 501–505]. Here, it is demonstrated that a complementary measure, the correlation of local r.m.s. density in adjacent regions on the unit cell, is also a good measure of the presence of distinct solvent and protein regions. The correlation of local r.m.s. density is essentially a measure of how contiguous the solvent (and protein) regions are in the electron-density map. This statistic can be calculated in real space or in reciprocal space and has potential uses in evaluation of heavy-atom solutions in the MIR and MAD methods as well as for evaluation of trial phase sets in ab initio phasing procedures.

scholarly journals Brickworxbuilds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

2015 ◽  
Vol 71 (3) ◽  
pp. 697-705 ◽  
Author(s):  
Grzegorz Chojnowski ◽  
Tomasz Waleń ◽  
Paweł Piątkowski ◽  
Wojciech Potrzebowski ◽  
Janusz M. Bujnicki
Keyword(s):  
Nucleic Acid ◽  
Electron Density ◽  
Three Dimensional ◽  
Real Space ◽  
Density Peaks ◽  
Density Maps ◽  
Resolution Electron ◽  
Fragment Library ◽  
Electron Density Map ◽  
Recurrent Motifs

Brickworxis a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure is RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. TheBrickworxprogram is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.

scholarly journals CT-guided bone biopsy using electron density maps from dual-energy CT

2021 ◽  
Vol 16 (9) ◽  
pp. 2343-2346
Author(s):  
Shota Yamamoto ◽  
Shunsuke Kamei ◽  
Kosuke Tomita ◽  
Chikara Fujita ◽  
Kazuyuki Endo ◽  
...  
Keyword(s):  
Electron Density ◽  
Bone Biopsy ◽  
Dual Energy ◽  
Dual Energy Ct ◽  
Ct Guided ◽  
Density Maps

A Comparison of Two Algorithms for Electron-Density Map Improvement by Introduction of Atomicity: Skeletonization, and Map Sorting Followed by Refinement

1998 ◽  
Vol 54 (1) ◽  
pp. 81-85 ◽  
Author(s):  
F. M. D. Vellieux
Keyword(s):  
Electron Density ◽  
Initial Density ◽  
Acta Cryst ◽  
Density Maps ◽  
Resolution Electron ◽  
Crystallographic Symmetry ◽  
Density Map ◽  
Ornithine Transcarbamoylase ◽  
Electron Density Map ◽  
Pseudo Atom

A comparison has been made of two methods for electron-density map improvement by the introduction of atomicity, namely the iterative skeletonization procedure of the CCP4 program DM [Cowtan & Main (1993). Acta Cryst. D49, 148–157] and the pseudo-atom introduction followed by the refinement protocol in the program suite DEMON/ANGEL [Vellieux, Hunt, Roy & Read (1995). J. Appl. Cryst. 28, 347–351]. Tests carried out using the 3.0 Å resolution electron density resulting from iterative 12-fold non-crystallographic symmetry averaging and solvent flattening for the Pseudomonas aeruginosa ornithine transcarbamoylase [Villeret, Tricot, Stalon & Dideberg (1995). Proc. Natl Acad. Sci. USA, 92, 10762–10766] indicate that pseudo-atom introduction followed by refinement performs much better than iterative skeletonization: with the former method, a phase improvement of 15.3° is obtained with respect to the initial density modification phases. With iterative skeletonization a phase degradation of 0.4° is obtained. Consequently, the electron-density maps obtained using pseudo-atom phases or pseudo-atom phases combined with density-modification phases are much easier to interpret. These tests also show that for ornithine transcarbamoylase, where 12-fold non-crystallographic symmetry is present in the P1 crystals, G-function coupling leads to the simultaneous decrease of the conventional R factor and of the free R factor, a phenomenon which is not observed when non-crystallographic symmetry is absent from the crystal. The method is far less effective in such a case, and the results obtained suggest that the map sorting followed by refinement stage should be by-passed to obtain interpretable electron-density distributions.

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