scholarly journals Protein crystallography in the 1970s: starting from scratch in a remote outpost

2014 ◽  
Vol 70 (a1) ◽  
pp. C933-C933
Author(s):  
Edward Baker
Keyword(s):  
Electron Density ◽  
Protein Crystallography ◽  
Data Sets ◽  
Acta Cryst ◽  
R Factor ◽  
The Difference ◽  
Do It Yourself ◽  
Sealed Source ◽  
The University ◽  
Electron Density Map

A conversation with Dorothy Hodgkin on a long bus trip, just before I returned to New Zealand in 1970, left me full of determination and optimism. This presentation will recount my experience in starting a protein crystallography lab with only a sealed-source generator and a precession camera for equipment. Crystals had to be large (0.5 - 1.0 mm on edge) and X-ray data, collected at room temperature on a borrowed small-molecule diffractometer, accumulated very slowly. We corrected for absorption and decay and scaled data sets rather crudely. It was very much a do-it-yourself environment. With no CCP4, software had to be borrowed or adapted or written oneself; methods papers in Acta Cryst. were like gold as I pored through them trying to understand. Communications with friends, by airmail, were vital. An electron density map for the cysteine protease actinidin, at 2.8 Å, was immediately interpretable thanks to excellent data and phases from more derivatives than were really necessary. An R factor of 42% to 2.0 Å, for a model built in a Richards box, was really quite astonishing. Later FFT-based least squares refinement at the University of York in 1978 was even more astonishing as the R factor rocketed down [1]. No computer graphics, but the difference electron density told the story – in retrospect there was even evidence that the crystals (prepared from kiwifruit bought at the local shop) contained several genetic variants of the protein! It may not have been the most exciting protein in the world (except to me!) but what a way to learn protein crystallography and protein structure.

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.

Correcting resolution bias in electron density maps of organic molecules derived by direct methods from powder data

2008 ◽  
Vol 41 (3) ◽  
pp. 592-599 ◽  
Author(s):  
Angela Altomare ◽  
Corrado Cuocci ◽  
Carmelo Giacovazzo ◽  
Anna Moliterni ◽  
Rosanna Rizzi
Keyword(s):  
Electron Density ◽  
Direct Methods ◽  
Large Set ◽  
Acta Cryst ◽  
Pattern Decomposition ◽  
Density Maps ◽  
Decomposition Procedure ◽  
Data Resolution ◽  
Current Electron ◽  
The Difference

Fourier syntheses providing electron density maps are usually affected by truncation effects due to the limited data resolution. A recent theoretical approach [Altomare, Cuocci, Giacovazzo, Kamel, Moliterni & Rizzi (2008).Acta Cryst.A64, 326–336] suggests that the resolution bias may be reduced by correcting the current electron density maps in accordance with the physics of the diffraction experiment. We have implemented the approach inEXPO2004[Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004).J. Appl. Cryst.37, 1025–1028], a program devoted to the solution of crystal structures from powder data. The new algorithm was applied at the end of the direct methods modulus, to verify if the reduction of the resolution bias is able to improve the electron density maps and to provide additional power to direct methods. Application of this method to a large set of test structures indicates that resolution-bias correction often makes the difference between success and failure, and thus constitutes a new tool for reducing the dependence of modern crystallography on resolution effects. The chances of failure are expected to depend on the quality of the experimental data (e.g.the accuracy of the full-pattern decomposition procedure and the data resolution), on the size of the structure and on its chemical composition.

Phase perturbation as a means of electron density map quality evaluation

2008 ◽  
Vol 41 (1) ◽  
pp. 31-37 ◽  
Author(s):  
Olga Kirillova
Keyword(s):  
Electron Density ◽  
Data Sets ◽  
Molecular Replacement ◽  
Data Set ◽  
Density Maps ◽  
Phase Perturbation ◽  
Replacement Solution ◽  
Electron Density Map ◽  
Trial Phase

This paper describes a new means for evaluating the quality of crystallographic electron density maps. It has been found that a better data set possesses greater robustness against perturbations applied to the phases. Thus it allows recognition of a more precise phase set and provides a way to select the best or reject the worst from several noisy data sets derived from the same crystal structure. The results indicate that calculation of the correlations by the procedure described here can be useful in ranking electron density maps in this aspect of quality. The method suggested has potential use for selecting a better molecular replacement solution, as well as for evaluating trial phase sets inab initiophasing procedures.

VLD algorithm and hybrid Fourier syntheses

2012 ◽  
Vol 45 (6) ◽  
pp. 1287-1294 ◽  
Author(s):  
Maria Cristina Burla ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori
Keyword(s):  
Electron Density ◽  
Standard Procedure ◽  
Joint Probability ◽  
Distribution Functions ◽  
Medium Size ◽  
Joint Probability Distribution ◽  
Fourier Synthesis ◽  
Acta Cryst ◽  
The Difference ◽  
Difference Fourier

The VLD (vive la difference) phasing algorithm combines the model electron density with the difference electron densityviareciprocal space relationships to obtain new phase values and drive them to the correct values. The process is iterative and has been applied to small and medium-size structures and to proteins. Hybrid Fourier syntheses show properties that are intermediate between those of the observed synthesis (whose peaks should correspond to the most probable atomic positions) and those of the difference synthesis (whose positive and negative peaks should correspond to missed atomic positions and to false atoms of the model, respectively). Thanks to these properties some hybrid syntheses can be used in the phase extension and refinement step, to reduce the model bias and more rapidly move to the target structure. They have been recently revisitedviathe method of joint probability distribution functions [Burla, Carrozzini, Cascarano, Giacovazzo & Polidori (2011).Acta. Cryst. A67, 447–455]. The results suggested that VLD could be usefully combined, forab initiophasing, with the hybrid rather than with the difference Fourier synthesis. This paper explores the feasibility of such a combination and shows that the original VLD algorithm is only one of several variants, all with relevant phasing capacity. The study explores the role of several parameters in order to design a standard procedure with optimized phasing power.

Anomalous dispersion analyses of the Ni-atom site in an aluminophosphate test crystal including the use of tuned synchrotron radiation

1996 ◽  
Vol 52 (3) ◽  
pp. 479-486 ◽  
Author(s):  
M. Helliwell ◽  
J. R. Helliwell ◽  
A. Cassetta ◽  
J. C. Hanson ◽  
T. Ericsson ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Data Sets ◽  
Acta Cryst ◽  
Data Set ◽  
Difference Map ◽  
Chemical Crystallography ◽  
Synchrotron Light ◽  
The Difference ◽  
Difference Fourier ◽  
Atom Position

Data were collected close to the Ni K edge, using synchrotron radiation at the National Synchrotron Light Source, and using a Mo Kα rotating anode, from a crystal of a nickel-containing aluminophosphate, NiAl3P4O18C4H21N4 (NiAPO). These data sets, along with an existing Cu Kα rotating anode data set, allowed the calculation of several f′ difference-Fourier maps exploiting the difference in f′ for Ni between the various wavelengths. These differences are expected to be 7.8, 4.5 and 3.3 e for Mo Kα data to SR (synchrotron radiation), Cu Kα to SR and Mo Kα to Cu Kα, respectively. The phases were calculated either excluding the Ni atom or with Al at the Ni-atom site. The f′ difference-Fourier maps revealed peaks at the Ni-atom site, whose height and distance from the refined Ni-atom position depended on the f' difference and the phase set used. The largest peak was located at a distance of only 0.025 Å from the refined Ni-atom site and was obtained from the f′ difference map calculated with the coefficients |F Mo Kα − F SR| , using phases calculated with Al at the Ni-atom site. In all cases, it was found that these phases gave optimal results without introducing bias into the maps. The results confirm and expand upon earlier results [Helliwell, Gallois, Kariuki, Kaučič & Helliwell (1993), Acta Cryst. B49, 420–428]. The techniques described are generally applicable to other systems containing anomalous scatterers in chemical crystallography.

scholarly journals Chlorido(pyridine-κN)(5,10,15,20-tetraphenylporphyrinato-κ4N)cobalt(III) chloroform hemisolvate

2012 ◽  
Vol 68 (8) ◽  
pp. m1104-m1105 ◽  
Author(s):  
Yassin Belghith ◽  
Jean-Claude Daran ◽  
Habib Nasri
Keyword(s):  
Bond Length ◽  
Electron Density ◽  
Title Complex ◽  
Acta Cryst ◽  
Π Interactions ◽  
The Difference ◽  
Difference Fourier ◽  
Atom Bond

In the title complex, [CoCl(C44H28N4)(C5H5N)]·0.5CHCl3or [CoIII(TPP)Cl(py)]·0.5CHCl3(where TPP is the dianion of tetraphenylporphyrin and py is pyridine), the average equatorial cobalt–pyrrole N atom bond length (Co—Np) is 1.958 (7) Å and the axial Co—Cl and Co—Npydistances are 2.2339 (6) and 1.9898 (17) Å, respectively. The tetraphenylporphyrinate dianion exhibits an important nonplanar conformation with major ruffling and saddling distortions. In the crystal, molecules are linkedviaweak C—H...π interactions. In the difference Fourier map, a region of highly disordered electron density was estimated using the SQUEEZE routine [PLATON; Spek (2009),Acta Cryst.D65, 148–155] to be equivalent to one half-molecule of CHCl3per molecule of the complex.

scholarly journals A pipeline for the rapid generation of difference maps from protein crystals

2014 ◽  
Vol 70 (a1) ◽  
pp. C1447-C1447 ◽  
Author(s):  
Marcin Wojdyr ◽  
Ronan Keegan ◽  
Graeme Winter ◽  
Alun Ashton ◽  
Andrey Lebedev ◽  
...  
Keyword(s):  
Electron Density ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Software Pipeline ◽  
The Difference ◽  
Rapid Generation ◽  
House Automation ◽  
Automated Software ◽  
Rapid Processing ◽  
Electron Density Map

"In 2013 MX beamlines at the Diamond synchrotron deployed an automated software pipeline, called DIMPLE, for rapid processing of crystals that contain a known protein and possibly a ligand bound. DIMPLE takes the already known ""apo"" structure for the target protein, compares it with the electron density map from X-ray diffraction images, and visualizes areas of the electron density unaccounted for by the structure model. When processing batches of crystals, such feedback allows the user to better decide what to measure next which leads to a more efficient use of the beam time. This year we've enhanced the pipeline to cover more complex cases, including changes in the space group and some changes in conformation. With multiple molecular replacement computations run in parallel, the time from shooting to viewing the difference map is still only a few minutes. While the software is developed primarily for use at synchrotron beamlines, it is included in the CCP4 suite and can be used as well for in-house automation."

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.

New algorithm for protein model building: extending a partial model in a map segment

2006 ◽  
Vol 39 (1) ◽  
pp. 57-63 ◽  
Author(s):  
Yong Zhou ◽  
Min Yao ◽  
Isao Tanaka
Keyword(s):  
Electron Density ◽  
Model Building ◽  
Threshold Value ◽  
Acta Cryst ◽  
Protein Model ◽  
Isolated Segment ◽  
Density Values ◽  
Density Map ◽  
Average Electron ◽  
Electron Density Map

An algorithm is presented for extending protein models in cases where only a partially built model is available. The problem can be viewed as linking and/or extending the existing separated model fragments in the electron density map. The process of solving this problem is divided into four steps. In the first step, the possible region for the missing part is extracted from an electron density map. For this purpose, the electron density map is first segmented through an electron density threshold value. The segment for the missing part is then isolated by removing the map region of the existing model. In the second step, two anchor positions are located within the isolated segment on the basis of the existing model: one representing the entry of the missing model and the other the exit. In the third step, a set of possible positions for Cαatoms of the extending residue are determined on the basis of the two anchor positions. In the fourth step, the best placement of the residue is found by ranking of the average electron density values. Steps three and four are repeated until all missing residues are built or no further extension is possible. The algorithm has been implemented in the programLAFIRE[Yao, Zhou & Tanaka (2006).Acta Cryst.D62, 189–196], which aims to automate the refinement process, and has been shown to be effective through tests.

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