scholarly journals Experimental phasing withSHELXC/D/E: combining chain tracing with density modification

2010 ◽  
Vol 66 (4) ◽  
pp. 479-485 ◽  
Author(s):  
George M. Sheldrick
Keyword(s):  
Main Chain ◽  
Heavy Atoms ◽  
General Account ◽  
Structure Solution ◽  
Experimental Phasing

The programsSHELXC, SHELXDandSHELXEare designed to provide simple, robust and efficient experimental phasing of macromolecules by the SAD, MAD, SIR, SIRAS and RIP methods and are particularly suitable for use in automated structure-solution pipelines. This paper gives a general account of experimental phasing using these programs and describes the extension of iterative density modification in SHELXEby the inclusion of automated protein main-chain tracing. This gives a good indication as to whether the structure has been solved and enables interpretable maps to be obtained from poorer starting phases. The autotracing algorithm starts with the location of possible seven-residue α-helices and common tripeptides. After extension of these fragments in both directions, various criteria are used to decide whether to accept or reject the resulting poly-Ala traces. Noncrystallographic symmetry (NCS) is applied to the traced fragments, not to the density. Further features are the use of a `no-go' map to prevent the traces from passing through heavy atoms or symmetry elements and a splicing technique to combine the best parts of traces (including those generated by NCS) that partly overlap.

scholarly journals The magic triangle goes MAD: experimental phasing with a bromine derivative

2010 ◽  
Vol 66 (4) ◽  
pp. 374-380 ◽  
Author(s):  
Tobias Beck ◽  
Tim Gruene ◽  
George M. Sheldrick
Keyword(s):  
Functional Groups ◽  
Heavy Atom ◽  
Anomalous Dispersion ◽  
Proteinase K ◽  
Nonspecific Binding ◽  
Heavy Atoms ◽  
Carboxylate Groups ◽  
Experimental Phasing ◽  
Sad Phasing ◽  
Bromine Derivative

Experimental 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 proteinsviahydrogen 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 incorporated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br Kedge was successfully 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.

Towards the automatic crystal structure solution of nucleic acids: automated model building using the new CAB program

2021 ◽  
Vol 77 (12) ◽  
Author(s):  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo
Keyword(s):  
Nucleic Acids ◽  
Prior Information ◽  
Model Building ◽  
Phase Error ◽  
Heavy Atoms ◽  
Density Maps ◽  
Structure Solution ◽  
Nucleic Acid Structures ◽  
Automated Model Building ◽  
Model Chain

CAB, a recently described automated model-building (AMB) program, has been modified to work effectively with nucleic acids. To this end, several new algorithms have been introduced and the libraries have been updated. To reduce the input average phase error, ligand heavy atoms are now located before starting the CAB interpretation of the electron-density maps. Furthermore, alternative approaches are used depending on whether the ligands belong to the target or to the model chain used in the molecular-replacement step. Robust criteria are then applied to decide whether the AMB model is acceptable or whether it must be modified to fit prior information on the target structure. In the latter case, the model chains are rearranged to fit prior information on the target chains. Here, the performance of the new AMB program CAB applied to various nucleic acid structures is discussed. Other well documented programs such as Nautilus, ARP/wARP and phenix.autobuild were also applied and the experimental results are described.

scholarly journals Softer but stronger? Sulfur SAD with low energy X-rays of 2.7 Å

2014 ◽  
Vol 70 (a1) ◽  
pp. C604-C604
Author(s):  
Dorothee Liebschner ◽  
Naohiro Matsugaki ◽  
Miki Senda ◽  
Yusuke Yamada ◽  
Toshiya Senda
Keyword(s):  
Absorption Edge ◽  
Protein Crystal ◽  
X Rays ◽  
Long Wavelength ◽  
Heavy Atoms ◽  
Statistical Validity ◽  
Experimental Phasing ◽  
Recent Developments ◽  
Long Time ◽  
Anomalous Signal

Single wavelength anomalous diffraction (SAD) is a powerful experimental phasing technique used in macromolecular crystallography (MX). SAD is based on the absorption of X-rays by heavy atoms, which can be either incorporated into the protein (crystal) or naturally present in the structure, such as sulfur or metal ions. In particular, sulfur seems to be an attractive candidate for phasing, because most proteins contain a considerable number of S atoms. However, the K-absorption edge of sulfur is around 5.1 Å wavelength (2.4 keV), which is far from the optimal wavelength of most MX-beamlines at synchrotrons. Therefore, phasing experiments have to be performed further away from the absorption edge, which results in weaker anomalous signal. This explains why S-SAD was not commonly used for a long time, although its feasibility was illustrated by the ground-breaking study by Hendrickson and Teeter [1]. Recent developments in instrumentation, software and methodology made it possible to measure intensities more accurately, and, as a consequence, S-SAD has lately obtained more and more attention [2]. The beamline BL-1A at Photon factory (KEK, Japan) is designed to take full advantage of a long wavelength X-ray beam at around 3 Å to further enhance anomalous signals. We performed S-SAD experiments at BL-1A using two different wavelengths (1.9 Å and 2.7 Å) and compared their phasing capabilities. This methodological study was performed with ferredoxin reductase crystals of various sizes. In order to guarantee statistical validity and to exclude the influence of a particular sample, we repeated the comparison with several crystals. The novelty in the approach consists in using very long wavelengths (2.7 Å), not fully exploited in the literature so far. According to our study, the 2.7 Å wavelength shows - despite strong absorption effects of the diffracted X-rays - more successful phasing results than at 1.9 Å.

On the application of phase relationships to complex structures. XIV. The additional use of statistical information in tangent-formula refinement

1978 ◽  
Vol 34 (6) ◽  
pp. 863-870 ◽  
Author(s):  
S. E. Hull ◽  
M. J. Irwin
Keyword(s):  
Computer Program ◽  
Computer Programs ◽  
Statistical Information ◽  
Complex Structures ◽  
Weighting Schemes ◽  
Heavy Atoms ◽  
Phase Development ◽  
Structure Solution ◽  
Unknown Structure ◽  
Phase Relationships

Suitable weighting schemes for use in tangent-formula phase development and refinement are discussed, and a statistically based weighting scheme, which can easily be incorporated in existing computer programs, is proposed. Examples of the use of this method in structure solution and completion are presented for a previously unknown structure and for several structures which had been difficult to solve by other methods. In addition a method is given for subtracting the contribution of heavy atoms from observed |E| values on a statistical basis which is very useful when the presence of such atoms leads to problems in defining the enantiomorph. These methods add greatly to the power of the MUL TAN computer program.

scholarly journals Molecular symmetry-constrained systematic search approach to structure solution of the coiled-coil SRGAP2 F-BARx domain

2016 ◽  
Vol 72 (12) ◽  
pp. 1241-1253 ◽  
Author(s):  
Michael Sporny ◽  
Julia Guez-Haddad ◽  
David G. Waterman ◽  
Michail N. Isupov ◽  
Yarden Opatowsky
Keyword(s):  
Diffraction Data ◽  
Coiled Coil ◽  
Systematic Search ◽  
Molecular Symmetry ◽  
Structure Solution ◽  
Experimental Phasing ◽  
Membrane Protrusions ◽  
Group A ◽  
Search Approach ◽  
Statistical Criteria

SRGAP2 (Slit–Robo GTPase-activating protein 2) is a cytoplasmic protein found to be involved in neuronal branching, restriction of neuronal migration and restriction of the length and density of dendritic postsynaptic spines. The extended F-BAR (F-BARx) domain of SRGAP2 generates membrane protrusions when expressed in COS-7 cells, while most F-BARs induce the opposite effect: membrane invaginations. As a first step to understand this discrepancy, the F-BARx domain of SRGAP2 was isolated and crystallized after co-expression with the carboxy domains of the protein. Diffraction data were collected from two significantly non-isomorphous crystals in the same monoclinicC2 space group. A correct molecular-replacment solution was obtained by applying a molecular symmetry-constrained systematic search approach that took advantage of the conserved biological symmetry of the F-BAR domains. It is shown that similar approaches can solve other F-BAR structures that were previously determined by experimental phasing. Diffraction data were reprocessed with a high-resolution cutoff of 2.2 Å, chosen using less strict statistical criteria. This has improved the outcome of multi-crystal averaging and other density-modification procedures.

Direct methods and simulated annealing: a hybrid approach for powder diffraction data

2008 ◽  
Vol 41 (1) ◽  
pp. 56-61 ◽  
Author(s):  
Angela Altomare ◽  
Rocco Caliandro ◽  
Corrado Cuocci ◽  
Carmelo Giacovazzo ◽  
Anna Grazia Giuseppina Moliterni ◽  
...  
Keyword(s):  
Simulated Annealing ◽  
Diffraction Data ◽  
Degrees Of Freedom ◽  
Molecular Model ◽  
Hybrid Approach ◽  
Direct Methods ◽  
Heavy Atoms ◽  
The Monte Carlo Method ◽  
Structure Solution ◽  
Electron Density Map

The solution of crystal structures from powder data using direct methods can be very difficult if the quality of the diffraction pattern is low and if no heavy atoms are present in the molecule. On the contrary, the use of direct-space methods does not require good quality diffraction data, but if a molecular model is available, the structure solution is limited principally by the number of degrees of freedom used to describe the model. The combination of the information contained in the electron density map (direct methods) with the Monte Carlo method, which uses simulated annealing as a global minimization algorithm (direct-space techniques), can be a useful tool for crystal structure solution, especially for organic structures. A modified and improved version of this approach [Altomareet al.(2003),J. Appl. Cryst.36, 230–238] has been implemented in theEXPO2004program and is described here.

scholarly journals Practical structure solution with ARCIMBOLDO

2012 ◽  
Vol 68 (4) ◽  
pp. 336-343 ◽  
Author(s):  
Dayté Rodríguez ◽  
Massimo Sammito ◽  
Kathrin Meindl ◽  
Iñaki M. de Ilarduya ◽  
Marianus Potratz ◽  
...  
Keyword(s):  
Main Chain ◽  
Experimental Information ◽  
Test Cases ◽  
Molecular Replacement ◽  
Sources Of Information ◽  
Parallel Processes ◽  
Structure Solution ◽  
Small Model ◽  
Α Helix ◽  
Distributed Test

Since its release in September 2009, the structure-solution program ARCIMBOLDO, based on the combination of locating small model fragments such as polyalanine α-helices with density modification with the program SHELXE in a multisolution frame, has evolved to incorporate other sources of stereochemical or experimental information. Fragments that are more sophisticated than the ubiquitous main-chain α-helix can be proposed by modelling side chains onto the main chain or extracted from low-homology models, as locally their structure may be similar enough to the unknown one even if the conventional molecular-replacement approach has been unsuccessful. In such cases, the program may test a set of alternative models in parallel against a specified figure of merit and proceed with the selected one(s). Experimental information can be incorporated in three ways: searching within ARCIMBOLDO for an anomalous fragment against anomalous differences or MAD data or finding model fragments when an anomalous substructure has been determined with another program such as SHELXD or is subsequently located in the anomalous Fourier map calculated from the partial fragment phases. Both sources of information may be combined in the expansion process. In all these cases the key is to control the workflow to maximize the chances of success whilst avoiding the creation of an intractable number of parallel processes. A GUI has been implemented to aid the setup of suitable strategies within the various typical scenarios. In the present work, the practical application of ARCIMBOLDO within each of these scenarios is described through the distributed test cases.

scholarly journals The MORPHEUS II protein crystallization screen

2015 ◽  
Vol 71 (7) ◽  
pp. 831-837 ◽  
Author(s):  
Fabrice Gorrec
Keyword(s):  
Protein Crystallization ◽  
Relative Yield ◽  
Protein Structure Determination ◽  
Data Bank ◽  
Buffer System ◽  
X Ray Diffraction ◽  
Heavy Atoms ◽  
Experimental Phasing ◽  
Crystallization Experiments ◽  
Broad Variety

High-quality macromolecular crystals are a prerequisite for the process of protein structure determination by X-ray diffraction. Unfortunately, the relative yield of diffraction-quality crystals from crystallization experiments is often very low. In this context, innovative crystallization screen formulations are continuously being developed. In the past, MORPHEUS, a screen in which each condition integrates a mix of additives selected from the Protein Data Bank, a cryoprotectant and a buffer system, was developed. Here, MORPHEUS II, a follow-up to the original 96-condition initial screen, is described. Reagents were selected to yield crystals when none might be observed in traditional initial screens. Besides, the screen includes heavy atoms for experimental phasing and small polyols to ensure the cryoprotection of crystals. The suitability of the resulting novel conditions is shown by the crystallization of a broad variety of protein samples and their efficiency is compared with commercially available conditions.

scholarly journals Phasertng: directed acyclic graphs for crystallographic phasing

2021 ◽  
Vol 77 (1) ◽  
pp. 1-10
Author(s):  
Airlie J. McCoy ◽  
Duncan H. Stockwell ◽  
Massimo D. Sammito ◽  
Robert D. Oeffner ◽  
Kaushik S. Hatti ◽  
...  
Keyword(s):  
Directed Acyclic Graph ◽  
Directed Acyclic Graphs ◽  
Molecular Replacement ◽  
Molecular Fragments ◽  
Graph Data ◽  
Acyclic Graphs ◽  
Structure Solution ◽  
Experimental Phasing ◽  
Graph Management ◽  
Extract Phase

Crystallographic phasing strategies increasingly require the exploration and ranking of many hypotheses about the number, types and positions of atoms, molecules and/or molecular fragments in the unit cell, each with only a small chance of being correct. Accelerating this move has been improvements in phasing methods, which are now able to extract phase information from the placement of very small fragments of structure, from weak experimental phasing signal or from combinations of molecular replacement and experimental phasing information. Describing phasing in terms of a directed acyclic graph allows graph-management software to track and manage the path to structure solution. The crystallographic software supporting the graph data structure must be strictly modular so that nodes in the graph are efficiently generated by the encapsulated functionality. To this end, the development of new software, Phasertng, which uses directed acyclic graphs natively for input/output, has been initiated. In Phasertng, the codebase of Phaser has been rebuilt, with an emphasis on modularity, on scripting, on speed and on continuing algorithm development. As a first application of phasertng, its advantages are demonstrated in the context of phasertng.xtricorder, a tool to analyse and triage merged data in preparation for molecular replacement or experimental phasing. The description of the phasing strategy with directed acyclic graphs is a generalization that extends beyond the functionality of Phasertng, as it can incorporate results from bioinformatics and other crystallographic tools, and will facilitate multifaceted search strategies, dynamic ranking of alternative search pathways and the exploitation of machine learning to further improve phasing strategies.

Crystal structure of the complex of 1,8-bis(dimethylamino)naphthalene with p-nitrosophenol by powder diffraction methods

2001 ◽  
Vol 216 (2) ◽  
Author(s):  
W. Lasocha ◽  
P. Milart ◽  
A. Rafalska-Łasocha ◽  
H. Schenk
Keyword(s):  
Crystal Structure ◽  
Organic Compounds ◽  
Powder Diffraction ◽  
Diffraction Method ◽  
Asymmetric Unit ◽  
Proton Sponge ◽  
Heavy Atoms ◽  
Structure Solution ◽  
Rigid Group

AbstractCrystal structure solution of organic compounds without heavy atoms by powder diffraction method is still a challenging task, particularly when there is not a rigid group in the compound, or when there are more than one molecule in the asymmetric unit. In this paper the crystal structure solution of the complex of “proton sponge” 1,8-bis(dimethylamino)naphthalene (DMAN) and

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