Molecular replacement: the approach of the programREMO

2006 ◽  
Vol 39 (2) ◽  
pp. 185-193 ◽  
Author(s):  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Liberato De Caro ◽  
Carmelo Giacovazzo ◽  
...  
Keyword(s):  
Fourier Transforms ◽  
Reciprocal Lattice ◽  
Correlation Factor ◽  
Test Problems ◽  
Model Structure ◽  
Molecular Replacement ◽  
Space Group ◽  
Model Molecule ◽  
Translation Function ◽  
Protein Space

A new program for molecular replacement,REMO, has been written. In the rotation step, the orientation of the model molecule is found by rotating the weighted reciprocal lattice of the protein with respect to the calculated transform of the model structure: the fitting is searched in the reciprocal space. The space group of the model structure is assumed to be the symmorphic variant of the protein space group. The algebra necessary to optimize the correlation factor between protein and model structure-factor moduli is described. The oriented model molecule is located by using the correlation function coupled with a translation function calculated by fast Fourier transforms.REMOhas been successfully applied to a variety of test problems and extensively compared with other currently available molecular replacement programs.

AUTOMR: an automatic processing program system for the molecular replacement method

1991 ◽  
Vol 24 (6) ◽  
pp. 1063-1066 ◽  
Author(s):  
Y. Matsuura
Keyword(s):  
Automatic Processing ◽  
Molecular Replacement ◽  
Initial Model ◽  
Program System ◽  
Replacement Method ◽  
Model Molecule ◽  
Translation Function ◽  
Processing Program ◽  
Molecular Replacement Method ◽  
Rotation Function

An automatic processing program system of the molecular replacement method AUTOMR is presented. The program solves the initial model of the target crystal structure using a homologous molecule as the search model. It processes the structure-factor calculation of the model molecule, the rotation function, the translation function and the rigid-group refinement successively in one computer job. Test calculations were performed for six protein crystals and the structures were solved in all of these cases.

scholarly journals X-ray crystal structure of a malonate-semialdehyde dehydrogenase fromPseudomonassp. strain AAC

2017 ◽  
Vol 73 (1) ◽  
pp. 24-28 ◽  
Author(s):  
Matthew Wilding ◽  
Colin Scott ◽  
Thomas S. Peat ◽  
Janet Newman
Keyword(s):  
Crystal Structure ◽  
Search Model ◽  
Molecular Replacement ◽  
X Rays ◽  
X Ray Diffraction ◽  
Acetyl Coa ◽  
Space Group ◽  
X Ray ◽  
Semialdehyde Dehydrogenase

The NAD-dependent malonate-semialdehyde dehydrogenase KES23460 fromPseudomonassp. strain AAC makes up half of a bicistronic operon responsible for β-alanine catabolism to produce acetyl-CoA. The KES23460 protein has been heterologously expressed, purified and used to generate crystals suitable for X-ray diffraction studies. The crystals belonged to space groupP212121and diffracted X-rays to beyond 3 Å resolution using the microfocus beamline of the Australian Synchrotron. The structure was solved using molecular replacement, with a monomer from PDB entry 4zz7 as the search model.

Mathematical aspects of molecular replacement. IV. Measure-theoretic decompositions of motion spaces

2017 ◽  
Vol 73 (5) ◽  
pp. 387-402 ◽  
Author(s):  
Gregory S. Chirikjian ◽  
Sajdeh Sajjadi ◽  
Bernard Shiffman ◽  
Steven M. Zucker
Keyword(s):  
General Theory ◽  
Rigid Body ◽  
Three Dimensional ◽  
Molecular Replacement ◽  
Translation Group ◽  
Common Occurrence ◽  
Space Group ◽  
Space Groups ◽  
Relevant Case ◽  
The Subject

In molecular-replacement (MR) searches, spaces of motions are explored for determining the appropriate placement of rigid-body models of macromolecules in crystallographic asymmetric units. The properties of the space of non-redundant motions in an MR search, called a `motion space', are the subject of this series of papers. This paper, the fourth in the series, builds on the others by showing that when the space group of a macromolecular crystal can be decomposed into a product of two space subgroups that share only the lattice translation group, the decomposition of the group provides different decompositions of the corresponding motion spaces. Then an MR search can be implemented by trading off between regions of the translation and rotation subspaces. The results of this paper constrain the allowable shapes and sizes of these subspaces. Special choices result when the space group is decomposed into a product of a normal Bieberbach subgroup and a symmorphic subgroup (which is a common occurrence in the space groups encountered in protein crystallography). Examples of Sohncke space groups are used to illustrate the general theory in the three-dimensional case (which is the relevant case for MR), but the general theory in this paper applies to any dimension.

Periodic Artifact Reduction in Fourier Transforms of Full Field Atomic Resolution Images

2015 ◽  
Vol 21 (2) ◽  
pp. 436-441 ◽  
Author(s):  
Robert Hovden ◽  
Yi Jiang ◽  
Huolin L. Xin ◽  
Lena F. Kourkoutis
Keyword(s):  
Fourier Transform ◽  
Boundary Conditions ◽  
Scanning Transmission Electron Microscopy ◽  
Fourier Transforms ◽  
Reciprocal Lattice ◽  
Atomic Resolution ◽  
Artifact Reduction ◽  
Full Field ◽  
Transmission Electron ◽  
Scanning Transmission

AbstractThe discrete Fourier transform is among the most routine tools used in high-resolution scanning/transmission electron microscopy (S/TEM). However, when calculating a Fourier transform, periodic boundary conditions are imposed and sharp discontinuities between the edges of an image cause a cross patterned artifact along the reciprocal space axes. This artifact can interfere with the analysis of reciprocal lattice peaks of an atomic resolution image. Here we demonstrate that the recently developed Periodic Plus Smooth Decomposition technique provides a simple, efficient method for reliable removal of artifacts caused by edge discontinuities. In this method, edge artifacts are reduced by subtracting a smooth background that solves Poisson’s equation with boundary conditions set by the image’s edges. Unlike the traditional windowed Fourier transforms, Periodic Plus Smooth Decomposition maintains sharp reciprocal lattice peaks from the image’s entire field of view.

scholarly journals Improved estimates of coordinate error for molecular replacement

2013 ◽  
Vol 69 (11) ◽  
pp. 2209-2215 ◽  
Author(s):  
Robert D. Oeffner ◽  
Gábor Bunkóczi ◽  
Airlie J. McCoy ◽  
Randy J. Read
Keyword(s):  
Molecular Replacement ◽  
Success Rates ◽  
Likelihood Functions ◽  
Sequence Identity ◽  
Protein Size ◽  
Translation Function ◽  
Essential Parameter ◽  
The Mean ◽  
Two Parameters

The estimate of the root-mean-square deviation (r.m.s.d.) in coordinates between the model and the target is an essential parameter for calibrating likelihood functions for molecular replacement (MR). Good estimates of the r.m.s.d. lead to good estimates of the variance term in the likelihood functions, which increases signal to noise and hence success rates in the MR search.Phaserhas hitherto used an estimate of the r.m.s.d. that only depends on the sequence identity between the model and target and which was not optimized for the MR likelihood functions. Variance-refinement functionality was added toPhaserto enable determination of the effective r.m.s.d. that optimized the log-likelihood gain (LLG) for a correct MR solution. Variance refinement was subsequently performed on a database of over 21 000 MR problems that sampled a range of sequence identities, protein sizes and protein fold classes. Success was monitored using the translation-functionZ-score (TFZ), where a TFZ of 8 or over for the top peak was found to be a reliable indicator that MR had succeeded for these cases with one molecule in the asymmetric unit. Good estimates of the r.m.s.d. are correlated with the sequence identity and the protein size. A new estimate of the r.m.s.d. that uses these two parameters in a function optimized to fit the mean of the refined variance is implemented inPhaserand improves MR outcomes. Perturbing the initial estimate of the r.m.s.d. from the mean of the distribution in steps of standard deviations of the distribution further increases MR success rates.

scholarly journals Purification, crystallization and initial crystallographic analysis of the α-catenin homologue HMP-1 fromCaenorhabditis elegans

2016 ◽  
Vol 72 (3) ◽  
pp. 234-239 ◽  
Author(s):  
Hyunook Kang ◽  
Injin Bang ◽  
William I. Weis ◽  
Hee-Jung Choi
Keyword(s):  
Crystallographic Analysis ◽  
Unit Cell ◽  
Molecular Replacement ◽  
Binding Region ◽  
Unit Cell Parameters ◽  
Mechanical Tension ◽  
Space Group ◽  
Cell Parameters ◽  
Terminal Domain ◽  
Mammalian Homologue

Adherens junctions transmit mechanical force between cells. In these junctions, β-catenin binds to cadherins and to the N-terminal domain of α-catenin, which in turn binds to actin filamentsviaits C-terminal domain. The middle (M) domain of α-catenin plays an important role in responding to mechanical tension. The nematodeCaenorhabditis eleganscontains α- and β-catenin homologues called HMP-1 and HMP-2, respectively, but HMP-1 behaves differently from its mammalian homologue. Thus, structural and biochemical studies of HMP-1 have been initiated to understand the mechanism of HMP-1 and the evolution of α-catenin. The N-terminal domain of HMP-1 in complex with the minimal HMP-1-binding region of HMP-2 was purified and crystallized. These crystals diffracted to 1.6 Å resolution and belonged to space groupP3121, with unit-cell parametersa=b= 57.1,c= 155.4 Å. The M domain of HMP-1 was also purified and crystallized. The M-domain crystals diffracted to 2.4 Å resolution and belonged to space groupP212121, with unit-cell parametersa = 72.8,b= 81.5,c = 151.4 Å. Diffraction data were collected and processed from each crystal, and the structures were solved by molecular replacement.

Mathematical aspects of molecular replacement. V. Isolating feasible regions in motion spaces

2020 ◽  
Vol 76 (2) ◽  
pp. 145-162
Author(s):  
Bernard Shiffman ◽  
Shengnan Lyu ◽  
Gregory S. Chirikjian
Keyword(s):  
Configuration Space ◽  
A Priori ◽  
Rigid Bodies ◽  
Molecular Replacement ◽  
Space Group ◽  
Fundamental Domains ◽  
Crystallographic Symmetry ◽  
Symmetry Constraints ◽  
Translation Space ◽  
The Right

This paper mathematically characterizes the tiny feasible regions within the vast 6D rotation–translation space in a full molecular replacement (MR) search. The capability to a priori isolate such regions is potentially important for enhancing robustness and efficiency in computational phasing in macromolecular crystallography (MX). The previous four papers in this series have concentrated on the properties of the full configuration space of rigid bodies that move relative to each other with crystallographic symmetry constraints. In particular, it was shown that the configuration space of interest in this problem is the right-coset space Γ\G, where Γ is the space group of the chiral macromolecular crystal and G is the group of rigid-body motions, and that fundamental domains F Γ\G can be realized in many ways that have interesting algebraic and geometric properties. The cost function in MR methods can be viewed as a function on these fundamental domains. This, the fifth and final paper in this series, articulates the constraints that bodies packed with crystallographic symmetry must obey. It is shown that these constraints define a thin feasible set inside a motion space and that they fall into two categories: (i) the bodies must not interpenetrate, thereby excluding so-called `collision zones' from consideration in MR searches; (ii) the bodies must be in contact with a sufficient number of neighbors so as to form a rigid network leading to a physically realizable crystal. In this paper, these constraints are applied using ellipsoidal proxies for proteins to bound the feasible regions. It is shown that the volume of these feasible regions is small relative to the total volume of the motion space, which justifies the use of ellipsoids as proxies for complex proteins in MR searches, and this is demonstrated with P1 (the simplest space group) and with P212121 (the most common space group in MX).

scholarly journals Nanoscale Order in Molecular Systems from Single Crystal Diffuse Scattering

2014 ◽  
Vol 67 (12) ◽  
pp. 1807 ◽  
Author(s):  
Darren J. Goossens ◽  
T. Richard Welberry
Keyword(s):  
Diffuse Scattering ◽  
Reciprocal Lattice ◽  
Local Order ◽  
Model Structure ◽  
Scattered Intensity ◽  
Great Strength ◽  
Crystalline Materials ◽  
Molecular Systems ◽  
Disordered Structures ◽  
Nanoscale Order

Diffuse scattering – the coherently scattered intensity that is not localised on the reciprocal lattice – contains a wealth of information about the local order (order on the nanoscale) in crystalline materials. Since molecules and atoms will respond most strongly to their local chemical environments, it is a valuable tool in understanding how structure leads to properties. However, at present its collection and analysis are relatively specialised. Monte Carlo (MC) computer simulation of a model structure has become a powerful and well-accepted technique for aiding the interpretation and analysis of diffuse scattering patterns. Its great strength is its flexibility – as long as an MC energy can be defined, a model can be developed and tested. At one extreme a very simplified model may be useful in demonstrating particular qualitative effects, while at the other a quantitative and very detailed description of disordered structures can be obtained. Examples discussed include new results concerning p-chloro-N-(p-chloro-benzylidene)aniline, a molecule showing various degrees of molecular flexibility.

λ/2 Contamination in charge-coupled-device area-detector data

1997 ◽  
Vol 30 (4) ◽  
pp. 514-516 ◽  
Author(s):  
K. Kirschbaum ◽  
A. Martin ◽  
A. A. Pinkerton
Keyword(s):  
Least Squares ◽  
Reciprocal Lattice ◽  
Routine Data ◽  
Intensity Increase ◽  
Data Sets ◽  
Charge Coupled Device ◽  
Space Group ◽  
Area Detector ◽  
Image Plate ◽  
Unit Cells

A method is proposed to estimate the amount of λ/2 contamination inherent in area-detector [charge-coupled device (CCD) or image plate] data using Mo radiation. The intensity increase due to the Mo λ/2 contribution to Ihkl has been determined by measurement of the intensity for reflections where h, k or l is half-integral, i.e. reflections where there is no contribution from λ, for three crystals using two different CCD diffractometers. This information is present in all data sets obtained with area detectors but is usually ignored. The correction thus determined has been applied to nine data sets. The improvement to the data, as measured from the least-squares refinement, is shown to be insignificant for routine data sets, even for the weak low-angle reflections. Some reduction in the number of `observed' systematic absences is noted, thus improving space-group assignments. In addition, for strongly diffracting crystals, incorrect unit cells may be obtained owing to the presence of strong λ/2 reflections at the reciprocal-lattice nodes.

Sign in / Sign up

Export Citation Format

Share Document