Shake‐and‐bake phasing methods have permitted the ab initio solution of crystal structures containing more than 1000 independent non‐H light atoms (C, N, O). The success of these procedures is ...critically dependent upon having diffraction data measured to at least 1.2 Å resolution. A new target function R2(ϕh) is introduced into the shake‐and‐bake procedure along with a real difference map strategy whereby this resolution limit can be appreciably lowered toward 1.5 Å. These improvements, when applied to moderately high resolution data, may now allow one the possibility to solve structures that are twice as large as could have been solved previously.
The crystal structure of the uncomplexed orthorhombic form of gramicidin A has been determined at 120 K and at 0.86 angstrom resolution. The pentadecapeptide crystallizes as a left-handed ...antiparallel double-stranded helical dimer with 5.6 amino acid residues per turn. The helix has an overall length of 31 angstroms and an average inner channel diameter of 4.80 angstroms. The channel of this crystalline form is void of ions or solvent molecules. The channel diameter varies form a minimum of 3.85 angstroms to a maximum of 5.47 angstroms and contains three pockets where the cross-channel contacts are 5.25 angstroms or greater. The range of variation seen for the φ and ψ torsion angles of the backbone of the helix suggests that these potential ion binding sites can be induced to travel the length of the channel in a peristaltic manner by cooperatively varying these angles. The indole rings of the eight tryptophan residues of the dimer are overlapped in three separate regions on the outer surface of the helix when viewed down the barrel of the channel. This arrangement would permit long-chained lipid molecules to nest parallel to the outer channel surface between these protruding tryptophan regions and act like molecular splines to constrain helical twist deformations of the channel.
The Shake-and-Bake method of structure determination is a new direct methods phasing algorithm based on a minimum-variance, phase invariant residual, which is referred to as the minimal principle. ...Previously, the algorithm had been applied only to known structures. This algorithm has now been applied to two previously unknown structures that contain 105 and 110 non-hydrogen atoms, respectively. This report focuses on (i) algorithmic and parametric optimizations of Shake-and-Bake and (ii) the determination of two previously unknown structures. Traditional tangent formula phasing techniques were unable to unravel these two new structures.
The fast Fourier transform (FFT) algorithm as normally formulated allows one to compute the Fourier transform of up to N complex structure factors, F(h), N/2 ≥h > −N/2, if the transform ρ(r) is ...computed on an N‐point grid. Most crystallographic FFT programs test the ranges of the Miller indices of the input data to ensure that the total number of grid divisions in the x, y and z directions of the cell is sufficiently large enough to perform the FFT. This note calls attention to a simple remedy whereby an FFT can be used to compute the transform on as coarse a grid as one desires without loss of precision.
The phase problem in neutron crystallography Hauptman, Herbert A.; Langs, David A.
Acta crystallographica. Section A, Foundations of crystallography,
20/May , Letnik:
59, Številka:
3
Journal Article
Recenzirano
The straightforward solution of the crystal structure of cyclosporin (C62H111N11O12·H2O) by a modified Shake‐and‐Bake procedure, using experimental neutron diffraction data alone, shows that the ...positivity of the density function is not a necessary prerequisite for solving the phase problem. The initial applications suggest the intriguing possibility that positivity may actually be a hindrance.
Oxazofurin is the inactive oxazole analogue of the C-glycosyl thiazole antitumor agent tiazofurin. Replacement of the thiazole sulfur in tiazofurin with the oxazole oxygen in oxazofurin produces ...conformational effects that are examined using crystallographic and computational methods. The crystal structure of oxazofurin contains six molecules in the asymmetric unit and has been refined to a standard R value of 6.8% for all data. The six oxazofurin conformers show an average C-glycosidic torsion angle of 70(9) degrees. This value is significantly higher than the average absolute C-glycosidic torsion angle of 24(10) degrees obtained from previous thiazole nucleoside structures. Previous studies suggest that, in tiazofurin, an electrostatic interaction between a positively charged thiazole sulfur and negatively charged furanose oxygen constrains the C-glycosidic torsion angle to a relatively small value. Ab initio molecular orbital studies presented here suggest that the higher C-glycosidic angles observed in the oxazofurin structures result from a repulsive interaction between negatively charged oxazole and furanose oxygens. Thus, it is likely that differences in activity between oxazo- and tiazofurin are either (1) due directly to differences in electronic properties between the thiazole and oxazole rings or (2) due to the variation in C-glycosidic bond conformation resulting from the alteration in the charge distribution of the heterocycle.
Single‐wavelength anomalous dispersion (SAS) data can in principle be phased by direct methods since a priori estimates of the three‐phase structure invariants can be computed from these data. The ...mean phase error of the most reliable triple estimates for a small protein, however, is typically no better than 60°, and does not bode well for applications to larger structures. A procedure is described that can substantially lower the error in these estimates and introduce a larger number of useful triple invariants into the phasing process. The mean phase error of the most reliable triples for a 2.5 Å resolution data set from a Pt derivative of a 115‐residue protein was reduced from 55 to 25° by this method. It was also possible to identify a significant number of the poorest triple estimates, those with mean phase errors approaching 90°, such that they could be reliably down‐weighted or excluded from the phasing process.
The presence of multiple alpha,alpha-dialkyl amino acids such as alpha-methylalanine (alpha-aminoisobutyric acid, Aib) leads to predominantly helical structures, either with alpha-helical or ...3(10)-helical hydrogen bonding patterns. The crystal structure of emerimicin-(1-9) benzyl ester (Ac-Phe-Aib-Aib-Aib-Val-Gly-Leu-Aib-Aib-OBzl) reported here shows essentially pure alpha-helical character, whereas other similar compounds show predominantly 3(10)-helical structures. The factors that govern helical preference include the inherent relative stability of the alpha-helix compared with the 3(10)-helix, the extra hydrogen bond seen with 3(10)-helices, and the enhanced electrostatic dipolar interaction of the 3(10)-helix when packed in a crystalline lattice. The balance of these forces, when combined with the steric requirements of the amino acid side chains, determines the relative stability of the two helical conformations under a given set of experimental conditions.
The linear pentadecapeptide antibiotic gramicidin D is a heterogeneous mixture of six components. Precise refinements of three-dimensional structures of naturally occurring gramicidin D in crystals ...obtained from methanol, ethanol, and n-propanol demonstrate the unexpected presence of stable left-handed antiparallel double-helical heterodimers that vary with the crystallization solvent. The side chains of Trp residues in the three structures exhibit sequence-specific patterns of conformational preference. Tyr substitution for Trp at position 11 appears to favor
β ribbon formation and stabilization of the antiparallel double helix that acts as a template for gramicidin folding and nucleation of different crystal forms. The fact that a minor component in a heterogeneous mixture influences aggregation and crystal nucleation has potential applications to other systems in which anomalous behavior is exhibited by aggregation of apparently homogeneous materials, such as the enigmatic behavior of prion proteins.
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