scholarly journals On the application of the expected log-likelihood gain to decision making in molecular replacement

2018 ◽  
Vol 74 (4) ◽  
pp. 245-255 ◽  
Author(s):  
Robert D. Oeffner ◽  
Pavel V. Afonine ◽  
Claudia Millán ◽  
Massimo Sammito ◽  
Isabel Usón ◽  
...  
Keyword(s):  
Decision Making ◽  
Measurement Errors ◽  
Single Atom ◽  
Molecular Replacement ◽  
Acta Cryst ◽  
Quickest Path ◽  
Experimental Phasing ◽  
Log Likelihood ◽  
Replacement Solution ◽  
Search Order

Molecular-replacement phasing of macromolecular crystal structures is often fast, but if a molecular-replacement solution is not immediately obtained the crystallographer must judge whether to pursue molecular replacement or to attempt experimental phasing as the quickest path to structure solution. The introduction of the expected log-likelihood gain [eLLG; McCoyet al.(2017),Proc. Natl Acad. Sci. USA,114, 3637–3641] has given the crystallographer a powerful new tool to aid in making this decision. The eLLG is the log-likelihood gain on intensity [LLGI; Read & McCoy (2016),Acta Cryst.D72, 375–387] expected from a correctly placed model. It is calculated as a sum over the reflections of a function dependent on the fraction of the scattering for which the model accounts, the estimated model coordinate error and the measurement errors in the data. It is shown how the eLLG may be used to answer the question `can I solve my structure by molecular replacement?'. However, this is only the most obvious of the applications of the eLLG. It is also discussed how the eLLG may be used to determine the search order and minimal data requirements for obtaining a molecular-replacement solution using a given model, and for decision making in fragment-based molecular replacement, single-atom molecular replacement and likelihood-guided model pruning.

scholarly journals The expected log-likelihood gain for decision making in molecular replacement

2018 ◽  
Vol 74 (a2) ◽  
pp. e411-e411
Author(s):  
Robert D. Oeffner ◽  
Pavel V. Afonine ◽  
Claudia Millán ◽  
Massimo Sammito ◽  
Isabel Usón ◽  
...  
Keyword(s):  
Decision Making ◽  
Molecular Replacement ◽  
Log Likelihood

scholarly journals Coping with strong translational noncrystallographic symmetry and extreme anisotropy in molecular replacement with Phaser: human Rab27a

2019 ◽  
Vol 75 (3) ◽  
pp. 342-353 ◽  
Author(s):  
Mostafa Jamshidiha ◽  
Inmaculada Pérez-Dorado ◽  
James W. Murray ◽  
Edward W. Tate ◽  
Ernesto Cota ◽  
...  
Keyword(s):  
Information Content ◽  
Measurement Errors ◽  
Primary Tumour ◽  
Free Form ◽  
Mutant Form ◽  
Rab Gtpases ◽  
Molecular Replacement ◽  
Data Set ◽  
Crystal Forms ◽  
Replacement Solution

Data pathologies caused by effects such as diffraction anisotropy and translational noncrystallographic symmetry (tNCS) can dramatically complicate the solution of the crystal structures of macromolecules. Such problems were encountered in determining the structure of a mutant form of Rab27a, a member of the Rab GTPases. Mutant Rab27a constructs that crystallize in the free form were designed for use in the discovery of drugs to reduce primary tumour invasiveness and metastasis. One construct, hRab27aMut, crystallized within 24 h and diffracted to 2.82 Å resolution, with a unit cell possessing room for a large number of protein copies. Initial efforts to solve the structure using molecular replacement by Phaser were not successful. Analysis of the data set revealed that the crystals suffered from both extreme anisotropy and strong tNCS. As a result, large numbers of reflections had estimated standard deviations that were much larger than their measured intensities and their expected intensities, revealing problems with the use of such data at the time in Phaser. By eliminating extremely weak reflections with the largest combined effects of anisotropy and tNCS, these problems could be avoided, allowing a molecular-replacement solution to be found. The lessons that were learned in solving this structure have guided improvements in the numerical analysis used in Phaser, particularly in identifying diffraction measurements that convey very little information content. The calculation of information content could also be applied as an alternative to ellipsoidal truncation. The post-mortem analysis also revealed an oversight in accounting for measurement errors in the fast rotation function. While the crystal of mutant Rab27a is not amenable to drug screening, the structure can guide new modifications to obtain more suitable crystal forms.

scholarly journals Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing

Crystals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 273
Author(s):  
Yoshita Srivastava ◽  
Rachel Bonn-Breach ◽  
Sai Shashank Chavali ◽  
Geoffrey M. Lippa ◽  
Jermaine L. Jenkins ◽  
...  
Keyword(s):  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Molecular Replacement ◽  
Hydrophobic Core ◽  
Anomalous Diffraction ◽  
Recognition Motif ◽  
Determination Process ◽  
Experimental Phasing ◽  
Crystal Contacts ◽  
Apical Loop

RNA plays a central role in all organisms and can fold into complex structures to orchestrate function. Visualization of such structures often requires crystallization, which can be a bottleneck in the structure-determination process. To promote crystallization, an RNA-recognition motif (RRM) of the U1A spliceosomal protein has been co-opted as a crystallization module. Specifically, the U1-snRNA hairpin II (hpII) single-stranded loop recognized by U1A can be transplanted into an RNA target to promote crystal contacts and to attain phase information via molecular replacement or anomalous diffraction methods using selenomethionine. Herein, we produced the F37M/F77M mutant of U1A to augment the phasing capability of this powerful crystallization module. Selenomethionine-substituted U1A(F37M/F77M) retains high affinity for hpII (KD of 59.7 ± 11.4 nM). The 2.20 Å resolution crystal structure reveals that the mutated sidechains make new S-π interactions in the hydrophobic core and are useful for single-wavelength anomalous diffraction. Crystals were also attained of U1A(F37M/F77M) in complex with a bacterial preQ1-II riboswitch. The F34M/F37M/F77M mutant was introduced similarly into a lab-evolved U1A variant (TBP6.9) that recognizes the internal bulged loop of HIV-1 TAR RNA. We envision that this short RNA sequence can be placed into non-essential duplex regions to promote crystallization and phasing of target RNAs. We show that selenomethionine-substituted TBP6.9(F34M/F37M/F77M) binds a TAR variant wherein the apical loop was replaced with a GNRA tetraloop (KD of 69.8 ± 2.9 nM), laying the groundwork for use of TBP6.9(F34M/F37M/F77M) as a crystallization module. These new tools are available to the research community.

Crystallization and preliminary X-ray diffraction studies of human catalase

1999 ◽  
Vol 55 (9) ◽  
pp. 1614-1615 ◽  
Author(s):  
R. A. P. Nagem ◽  
E. A. L. Martins ◽  
V. M. Gonçalves ◽  
R. Aparício ◽  
I. Polikarpov
Keyword(s):  
Search Model ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
Beef Liver ◽  
X Ray ◽  
Diffusion Technique ◽  
Cell Dimensions ◽  
Synchrotron Radiation Diffraction ◽  
Replacement Solution ◽  
Unit Cell Dimensions

The enzyme catalase (H2O2–H2O2 oxidoreductase; E.C. 11.1.6) was purified from haemolysate of human placenta and crystallized using the vapour-diffusion technique. Synchrotron-radiation diffraction data have been collected to 1.76 Å resolution. The enzyme crystallized in the space group P212121, with unit-cell dimensions a = 83.6, b = 139.4, c = 227.5 Å. A molecular-replacement solution of the structure has been obtained using beef liver catalase (PDB code 4blc) as a search model.

scholarly journals Using a partial atomic model from medium-resolution cryo-EM to solve a large crystal structure

2021 ◽  
Vol 77 (1) ◽  
pp. 11-18
Author(s):  
Montserrat Fàbrega-Ferrer ◽  
Ana Cuervo ◽  
Francisco J. Fernández ◽  
Cristina Machón ◽  
Rosa Pérez-Luque ◽  
...  
Keyword(s):  
Molecular Replacement ◽  
Large Crystal ◽  
Rotation Matrices ◽  
Cryo Electron Microscopy ◽  
Partial Models ◽  
Medium Resolution ◽  
Experimental Phasing ◽  
Crystallographic Structures ◽  
Direct Use ◽  
Rotation Function

Medium-resolution cryo-electron microscopy maps, in particular when they include a significant number of α-helices, may allow the building of partial models that are useful for molecular-replacement searches in large crystallographic structures when the structures of homologs are not available and experimental phasing has failed. Here, as an example, the solution of the structure of a bacteriophage portal using a partial 30% model built into a 7.8 Å resolution cryo-EM map is shown. Inspection of the self-rotation function allowed the correct oligomerization state to be determined, and density-modification procedures using rotation matrices and a mask based on the cryo-EM structure were critical for solving the structure. A workflow is described that may be applicable to similar cases and this strategy is compared with direct use of the cryo-EM map for molecular replacement.

Sensor-Based Decision Making in Uncertain Context

2017 ◽  
pp. 234-257
Author(s):  
Eric Villeneuve ◽  
François Pérès ◽  
Cedrik Beler ◽  
Vicente González-Prida
Keyword(s):  
Decision Making ◽  
Network Architecture ◽  
Measurement Errors ◽  
False Negative ◽  
Decision Makers ◽  
Organizational Network ◽  
Decision Aiding ◽  
External Impact ◽  
Information Collecting ◽  
Embedded Intelligence

Decision makers, whether human or computer, using sensor networks to instrument information collecting necessary for decision, often face difficulties in assessing confidence granted to signals transmitted and received in the network. Several organizational (network architecture or nature, distance between sensors ...), internal (sensor reliability or accuracy ...) or external (impact of environment ...) factors can lead to measurement errors (false alarm, non-detection by misinterpretation of the analyzed signals, false-negative …). A system-embedded intelligence is then necessary, to compare the information received for the purpose of decision aiding based on margin of errors converted in confidence intervals. In this chapter, the authors present four complementary approaches to quantify the interpretation of signals exchanged in a network of sensors in the presence of uncertainty.

scholarly journals Crystallization and molecular-replacement solution of a diagnostic fluorescent dye in complex with a specific Fab fragment

2007 ◽  
Vol 63 (3) ◽  
pp. 217-223 ◽  
Author(s):  
Roman C. Hillig ◽  
Siegfried Baesler ◽  
Stefanie Urlinger ◽  
Yvonne Stark ◽  
Susanne Bauer ◽  
...  
Keyword(s):  
Fluorescent Dye ◽  
Molecular Replacement ◽  
Fab Fragment ◽  
Replacement Solution

Leishmania mexicana mexicanaglucose-6-phosphate isomerase: crystallization, molecular-replacement solution and inhibition

2004 ◽  
Vol 60 (5) ◽  
pp. 915-919 ◽  
Author(s):  
Artur T. Cordeiro ◽  
Renaud Hardré ◽  
Paul A. M. Michels ◽  
Laurent Salmon ◽  
Luis F. Delboni ◽  
...  
Keyword(s):  
Molecular Replacement ◽  
Leishmania Mexicana ◽  
Replacement Solution

Crystallization, molecular replacement solution, and refinement of tetrameric β-amylase from sweet potato

1995 ◽  
Vol 21 (2) ◽  
pp. 105-117 ◽  
Author(s):  
Cheom Gil Cheong ◽  
Soo Hyun Eom ◽  
Changsoo Chang ◽  
Dong Hae Shin ◽  
Hyun Kyu Song ◽  
...  
Keyword(s):  
Sweet Potato ◽  
Molecular Replacement ◽  
Replacement Solution

The molecular-replacement solution of an intermediate-sized helical polypeptide, antiamoebin I

1999 ◽  
Vol 55 (9) ◽  
pp. 1539-1545 ◽  
Author(s):  
C. F. Snook ◽  
B. A. Wallace
Keyword(s):  
Careful Consideration ◽  
Molecular Replacement ◽  
Helix Axis ◽  
Asymmetric Unit ◽  
High Resolution Data ◽  
Symmetric Structure ◽  
Structure Factors ◽  
Replacement Solution ◽  
Independent Molecules ◽  
Starting Model

The successful use of molecular-replacement methods for the solution of the intermediate-sized helical polypeptide antiamoebin I required the careful consideration of a number of parameters and exhibited some unusual characteristics when compared with molecular-replacement solutions of globular proteins. High-resolution data were required owing to several features, including the comma-like shape of the molecule (which results in a pseudo-symmetric structure at low resolution), the relative uniformity of the structure in the direction along the helix axis and the small differences between the two independent molecules in the P1 asymmetric unit. Other parameters which were important for the solution of this relatively low solvent content closely packed cell included the radius of integration, the use of normalized structure factors and especially the choice of starting model.

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