scholarly journals Automated MAD and MIR structure solution

1999 ◽  
Vol 55 (4) ◽  
pp. 849-861 ◽  
Author(s):  
Thomas C. Terwilliger ◽  
Joel Berendzen
Keyword(s):  
Model Building ◽  
Heavy Atom ◽  
Solution Process ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Major Step ◽  
Subjective Evaluations ◽  
Structure Solution ◽  
Structure Determinations ◽  
Genomic Scale

Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations.

scholarly journals Exploiting subtle structural differences in heavy-atom derivatives for experimental phasing

2014 ◽  
Vol 70 (7) ◽  
pp. 1873-1883 ◽  
Author(s):  
Jimin Wang ◽  
Yue Li ◽  
Yorgo Modis
Keyword(s):  
Structure Determination ◽  
Heavy Atom ◽  
Data Sets ◽  
Diarrhea Virus ◽  
Isomorphous Replacement ◽  
Experimental Phasing ◽  
Structural Differences ◽  
Structure Determinations ◽  
Weak Derivatives ◽  
Viral Diarrhea Virus

Structure determination using the single isomorphous replacement (SIR) or single-wavelength anomalous diffraction (SAD) methods with weak derivatives remains very challenging. In a recent structure determination of glycoprotein E2 from bovine viral diarrhea virus, three isomorphous uranium-derivative data sets were merged to obtain partially interpretable initial experimental maps. Small differences between them were then exploited by treating them as three independent SAD data sets plus three circular pairwise SIR data sets to improve the experimental maps. Here, how such subtle structural differences were exploited for experimental phasing is described in detail. The basis for why this approach works is also provided: the effective resolution of isomorphous signals between highly isomorphous derivatives is often much higher than the effective resolution of the anomalous signals of individual derivative data sets. Hence, the new phasing approaches outlined here will be generally applicable to structure determinations involving weak derivatives.

scholarly journals Structure for the N-terminal domain of HCV glycoprotein E1

2014 ◽  
Vol 70 (a1) ◽  
pp. C1803-C1803
Author(s):  
Kamel El Omari ◽  
Oleg Iourin ◽  
Jan Kadlec ◽  
Geoff Sutton ◽  
Richard Fearn ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Model Building ◽  
Heavy Atom ◽  
Protein Fold ◽  
X Ray ◽  
Terminal Domain ◽  
Structure Solution ◽  
Phase Extension ◽  
Resolution Model ◽  
Covalently Linked

Single-wavelength anomalous dispersion of sulfur atoms (S-SAD) is an elegant phasing method to determine crystal structures that does not require heavy atom incorporation or selenomethionine derivatization. Nevertheless this technique has been limited by the paucity of the signal at usual X-ray wavelengths, requiring very accurate measurement of the anomalous differences. Here we report the data collection and structure solution of the N-terminal domain of the ectodomain of Hepatitis C virus (HCV) E1, from crystals that diffracted very weakly. By combining the data from 32 crystals it was possible to solve the sulfur substructure and calculate initial maps at 7Å resolution, and after density modification and phase extension, using a higher resolution native dataset, to 3.5Å resolution, model building was achievable. The crystal structure of the N-terminal domain of reveals a complex network of covalently linked intertwined homodimers that do not harbor the expected truncated class II fusion protein fold.

scholarly journals Synchrotron-based macromolecular crystallography module for an undergraduate biochemistry laboratory course

2016 ◽  
Vol 49 (6) ◽  
pp. 2235-2243 ◽  
Author(s):  
Kyle M. Stiers ◽  
Christopher B. Lee ◽  
Jay C. Nix ◽  
John J. Tanner ◽  
Lesa J. Beamer
Keyword(s):  
Diffraction Data ◽  
Model Building ◽  
Data Sets ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Synchrotron Source ◽  
Undergraduate Laboratory ◽  
Laboratory Component ◽  
Set Up ◽  
Protein Models

This paper describes the introduction of synchrotron-based macromolecular crystallography (MX) into an undergraduate laboratory class. An introductory 2 week experimental module on MX, consisting of four laboratory sessions and two classroom lectures, was incorporated into a senior-level biochemistry class focused on a survey of biochemical techniques, including the experimental characterization of proteins. Students purified recombinant protein samples, set up crystallization plates and flash-cooled crystals for shipping to a synchrotron. Students then collected X-ray diffraction data sets from their crystalsviathe remote interface of the Molecular Biology Consortium beamline (4.2.2) at the Advanced Light Source in Berkeley, CA, USA. Processed diffraction data sets were transferred back to the laboratory and used in conjunction with partial protein models provided to the students for refinement and model building. The laboratory component was supplemented by up to 2 h of lectures by faculty with expertise in MX. This module can be easily adapted for implementation into other similar undergraduate classes, assuming the availability of local crystallographic expertise and access to remote data collection at a synchrotron source.

scholarly journals Temperature dependence of Uiso constraints in riding hydrogen treatments

2014 ◽  
Vol 70 (a1) ◽  
pp. C286-C286
Author(s):  
Jens Luebben ◽  
Simon Grabowsky ◽  
Alison Edwards ◽  
Wolfgang Morgenroth ◽  
George Sheldrick ◽  
...  
Keyword(s):  
Temperature Dependence ◽  
Structure Refinement ◽  
Heavy Atom ◽  
Data Sets ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Structure Determinations ◽  
Thermal Displacements ◽  
Conventional Structure ◽  
Oniom Approach

"Anisotropic parametrisation of the thermal displacements of hydrogen atoms in single-crystal X-ray structure refinement is not possible with independent atom model (IAM) scattering factors. This is due to the weak scattering contribution of hydrogen atoms. Only when aspherical scattering factors are used can carefully measured Bragg data provide such information. For conventional structure determinations parameters of ""riding"" hydrogen atoms are frequently constrained to values of their ""parent"" heavy atom. Usually values of 1.2 and 1.5 times X-U_eq are assigned to H-U_iso in these cases. Such constraints yield reasonable structural models for room-temperature data. However, todays small molecule X-Ray diffraction experiments are usually carried out at significantly lower temperatures. To further study the temperature dependence of ADPs we have evaluated several data sets of N-Acetyl-L-4-Hydroxyproline Monohydrate at temperatures ranging from 9 K to 250 K. Methods compared were HAR [1], Invariom refinement [2], time-of-flight Neutron diffraction and the TLS+ONIOM approach [3]. In the TLS+ONIOM approach non-hydrogen ADPs from Invariom refinement provided ADPs for the TLS-fit. Hydrogen atoms in all methods were grouped and analyzed according to their Invariom name. We reach a good agreement of the temperature dependence of H-U_iso/X-U_eq. At very low temperatures the ratio H-U_iso/X-U_eq can be as high as 4, e.g. for Hydrogen attached to a sp3 carbon atom with three non-Hydrogen atom neighbors. Since all methods consistently show that the H-U_iso/X-U_eq ratio is temperature dependent, this effect should be taken into account in conventional structure determinations."

scholarly journals Pushing the limits of sulfur SAD phasing:de novostructure solution of the N-terminal domain of the ectodomain of HCV E1

2014 ◽  
Vol 70 (8) ◽  
pp. 2197-2203 ◽  
Author(s):  
Kamel El Omari ◽  
Oleg Iourin ◽  
Jan Kadlec ◽  
Richard Fearn ◽  
David R. Hall ◽  
...  
Keyword(s):  
Data Collection ◽  
Crystal Structures ◽  
Model Building ◽  
Heavy Atom ◽  
Data Set ◽  
X Ray ◽  
Terminal Domain ◽  
Structure Solution ◽  
Phase Extension ◽  
Resolution Model

Single-wavelength anomalous dispersion of S atoms (S-SAD) is an elegant phasing method to determine crystal structures that does not require heavy-atom incorporation or selenomethionine derivatization. Nevertheless, this technique has been limited by the paucity of the signal at the usual X-ray wavelengths, requiring very accurate measurement of the anomalous differences. Here, the data collection and structure solution of the N-terminal domain of the ectodomain of HCV E1 from crystals that diffracted very weakly is reported. By combining the data from 32 crystals, it was possible to solve the sulfur substructure and calculate initial maps at 7 Å resolution, and after density modication and phase extension using a higher resolution native data set to 3.5 Å resolution model building was achievable.

A new parallel and GPU version of aTREOR-based algorithm for indexing powder diffraction data

2015 ◽  
Vol 48 (1) ◽  
pp. 166-170 ◽  
Author(s):  
Ivan Šimeček ◽  
Jan Rohlíček ◽  
Tomáš Zahradnický ◽  
Daniel Langr
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Graphics Processing Units ◽  
Solution Process ◽  
Data Sets ◽  
Powder Diffraction Data ◽  
Structure Solution ◽  
Indexing Method ◽  
Brute Force Approach ◽  
Graphics Processing

One of the key parts of the crystal structure solution process from powder diffraction data is indexing – the determination of the lattice parameters from experimental data. This paper presents a modification of theTREORindexing method that makes the algorithm suitable and efficient for execution on graphics processing units. TheTREORalgorithm was implemented in its pure form, which can be simply described as a `brute-force' approach. The effectiveness and time consumption of such an algorithm was tested on several data sets including monoclinic and triclinic examples. The results show the potential of using GPUs for indexing powder diffraction data.

Isomorphous replacement in electron diffraction of wet crystals of rat hemoglobin

1983 ◽  
Vol 41 ◽  
pp. 446-447
Author(s):  
William F. Tivol ◽  
Murray Vernon King ◽  
D. F. Parsons
Keyword(s):  
Electron Diffraction ◽  
Heavy Atom ◽  
Isomorphous Substitution ◽  
X Ray Diffraction ◽  
Salt Solutions ◽  
X Ray ◽  
Isomorphous Replacement ◽  
Structure Factors ◽  
Diffraction Structure ◽  
The Mean

Feasibility of isomorphous substitution in electron diffraction is supported by a calculation of the mean alteration of the electron-diffraction structure factors for hemoglobin crystals caused by substituting two mercury atoms per molecule, following Green, Ingram & Perutz, but with allowance for the proportionality of f to Z3/4 for electron diffraction. This yields a mean net change in F of 12.5%, as contrasted with 22.8% for x-ray diffraction.Use of the hydration chamber in electron diffraction opens prospects for examining many proteins that yield only very thin crystals not suitable for x-ray diffraction. Examination in the wet state avoids treatments that could cause translocation of the heavy-atom labels or distortion of the crystal. Combined with low-fluence techniques, it enables study of the protein in a state as close to native as possible.We have undertaken a study of crystals of rat hemoglobin by electron diffraction in the wet state. Rat hemoglobin offers a certain advantage for hydration-chamber work over other hemoglobins in that it can be crystallized from distilled water instead of salt solutions.

scholarly journals High-pressure synthesis of REB5O8(OH)2 (RE = Ho, Er, Tm)

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Michael Zoller ◽  
Hubert Huppertz
Keyword(s):  
High Pressure ◽  
Rare Earth ◽  
Ir Spectroscopy ◽  
Earth Metal ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Solution ◽  
Pressure Synthesis ◽  
The Rare Earth

AbstractThe rare earth oxoborates REB5O8(OH)2 (RE = Ho, Er, Tm) were synthesized in a Walker-type multianvil apparatus at a pressure of 2.5 GPa and a temperature of 673 K. Single-crystal X-ray diffraction data provided the basis for the structure solution and refinement. The compounds crystallize in the monoclinic space group C2 (no. 5) and are composed of a layer-like structure containing dreier and sechser rings of corner sharing [BO4]5− tetrahedra. The rare earth metal cations are coordinated between two adjacent sechser rings. Further characterization was performed utilizing IR spectroscopy.

scholarly journals High-pressure synthesis and characterization of the non-centrosymmetric scandium borate ScB6O9(OH)3

2020 ◽  
Vol 75 (6-7) ◽  
pp. 597-603
Author(s):  
Birgit Fuchs ◽  
Hubert Huppertz
Keyword(s):  
High Pressure ◽  
High Temperature ◽  
Synthesis And Characterization ◽  
X Ray Diffraction ◽  
X Ray ◽  
High Pressure High Temperature ◽  
Structure Solution ◽  
Temperature Experiment ◽  
Pressure Synthesis

AbstractThe non-centrosymmetric scandium borate ScB6O9(OH)3 was obtained through a high-pressure/high-temperature experiment at 6 GPa and 1473 K. Single-crystal X-ray diffraction revealed that the structure is isotypic to InB6O9(OH)3 containing borate triple layers separated by scandium layers. The compound crystallizes in the space group Fdd2 with the lattice parameters a = 38.935(4), b = 4.4136(4), and c = 7.6342(6) Å. Powder X-ray diffraction and vibrational spectroscopy were used to further characterize the compound and verify the proposed structure solution.

scholarly journals Optimization in S-SAD phasing - difference between solved and unsolved structure

2014 ◽  
Vol 70 (a1) ◽  
pp. C613-C613
Author(s):  
Jan Stránský ◽  
Tomáš Kovaľ ◽  
Lars Østergaard ◽  
Jarmila Dušková ◽  
Tereza Skálová ◽  
...  
Keyword(s):  
Data Processing ◽  
De Novo ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Solution ◽  
Sad Phasing ◽  
Optimal Values ◽  
Grant Agency ◽  
Intensity Reading

Development of X-ray diffraction technologies have made de novo phasing of protein structures by single-wavelength anomalous dispersion by sulphur (S-SAD) more common. As anomalous differences in the sulphur atomic factors are in the order of errors of measurement, careful intensity reading and data processing are crucial. S-SAD was used for de novo phasing of a small 12 kDa protein with 4 sulphur atoms per molecule at 2.3 Å, where the data did not enable a straightforward structure solution. Data processing was performed using XDS [1] and scaling using XSCALE. The sulphur substructure was determined by SHELXD [2] and phases were obtained from SHELXE [2]. Both algorithms strongly depend on input parameters and default values did not lead to the correct phases. Therefore a systematic search of optimal values of several parameters was used to find a solution. This method helped to confirm sulphur substructure and to differentiate the handedness of the solutions. Moreover, a script for comfortable conversion of SHELX outputs to MTZ format was developed, using programmes included in the CCP4 package [3]. The previously unsolvable protein structure was successfully resolved with the described procedure. This work was supported by the Grant Agency of the Czech Technical University in Prague, (SGS13/219/OHK4/3T/14), the Czech Science Foundation (P302/11/0855), project BIOCEV CZ.1.05/1.1.00/02.0109 from the ERDF.

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