<i>JBluIce–EPICS</i>control system for macromolecular crystallography

Степанов, С. А.; Макаров, О. А.; Hilgart, Mark; Pothineni, Sudhir Babu; Urakhchin, Alex; Devarapalli, Satish; Yoder, Derek W.; Becker, Michael E.; Ogata, Craig M.; Sanishvili, Ruslan; Venugopalan, Nagarajan; Smith, Janet L.; Fischetti, Robert F.

doi:10.1107/s0907444910053916

Cited by 47 publications

(40 citation statements)

References 27 publications

(34 reference statements)

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“…Most crystals diffracted to 2.2–2.5 Å resolution when exposed to 0.3 s of unattenuated beam using 0.3° oscillations. To mitigate radiation damage, a continuous (helical vector) data collection mode was employed (Stepanov et al, 2011). A 99.1% complete data set at 2.2 Å resolution was obtained by merging data from 10 crystals, using XDS (Kabsch, 2010) and Aimless (Winn et al, 2011).…”

Section: Star*methodsmentioning

confidence: 99%

Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV

et al. 2017

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Summary CCR5 is the primary chemokine receptor utilized by HIV to infect leukocytes, whereas CCR5 ligands inhibit infection by blocking CCR5 engagement with HIV gp120. To guide the design of improved therapeutics, we solved the structure of CCR5 in complex with chemokine antagonist [5P7]CCL5. Several structural features appeared to contribute to the anti-HIV potency of [5P7]CCL5, including the distinct chemokine orientation relative to the receptor, the near-complete occupancy of the receptor binding pocket, the dense network of intermolecular hydrogen bonds, and the similarity of binding determinants with the FDA-approved HIV inhibitor Maraviroc. Molecular modeling indicated that HIV gp120 mimicked the chemokine interaction with CCR5, providing an explanation for the ability of CCR5 to recognize diverse ligands and gp120 variants. Our findings reveal that structural plasticity facilitates receptor-chemokine specificity and enables exploitation by HIV, and provide insight into the design of small molecule and protein inhibitors for HIV and other CCR5-mediated diseases.

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Section: Star*methodsmentioning

confidence: 99%

Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV

et al. 2017

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“…At the National Institute of General Medical Sciences and National Cancer Institute Structural Biology Facility at the Advanced Photon Source (GM/CA@APS), we developed the quad-mini-beam collimator that allowed users to rapidly select a 5, 10, or 20 μm diameter beam or a larger variable beam size with a scatter guard aperture [2,3]. We also developed the JBluIce-EPICS GUI and software tools that allow users to fully exploit the rapid beam size change [4,5]. These tools have been applied to challenging projects and resulted in the determination of several high impact structures [for example, 6,7,8,9].…”

Section: Introductionmentioning

confidence: 99%

Predicted optical performance of the GM/CA@APS micro-focus beamline

Fischetti

Yoder

et al. 2013

J. Phys.: Conf. Ser.

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GM/CA at the APS has developed microcrystallography capabilities for structural biology applications. The robust, quad, mini-beam collimators, which enable users to rapidly select between a 5, 10 or 20 micron diameter beam or a scatter guard for the full focused beam, are coupled with several powerful automated software tools that are built into the beamline control system JBluIce-EPICS. Recent successes at beamlines around the world in solving structures from microcrystals (2 – 10 microns) have led to increased demand for high-intensity micro-focus beams. We have designed a new micro-focus endstation to increase the intensity in mini- and micro-beams at GM/CA by one to two orders of magnitude to meet this growing demand. The new optical design is based on the well-established approach of using two-stage demagnification. The existing bimorph mirrors, arranged in a Kirkpatrick-Baez geometry, focus the beam onto slits located upstream of the sample whereby the slit aperture defines a secondary source, that is reimaged with a second pair of mirrors. This design incorporates two focal modes: a mini-beam mode where the beam is focused to 20-micron diameter and a micro-beam mode where it is focused to 5-microns. The size of the secondary source aperture can be varied rapidly (seconds) to adjust the beam size at the sample position in two ranges 20 – 3 micron and 5 – 1 micron. The second set of mirrors will each have two super polished ellipses allowing quick (minutes) interchange between modes.

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“…change the energy and realign the beamline optical components and sample environment) at each wavelength at which MAD data were collected. The degree of automation achieved during the last decade at the ESRF MX beamlines (Arzt et al, 2005) and at other synchrotrons worldwide (Soltis et al, 2008;Stepanov et al, 2011;Cork et al, 2006) has simplified and stabilized the operation of tunable MX beamlines to the extent that energy changes during MAD experiments are now almost transparent to the user. This increase in userfriendliness has allowed users to concentrate on the optimization of experiment design, which is particularly relevant when extracting small anomalous signals for de novo structure solution or when samples are sensitive to radiation damage.…”

Section: Interleaved Mad Data Collectionmentioning

confidence: 99%

Facilitating best practices in collecting anomalous scattering data forde novostructure solution at the ESRF Structural Biology Beamlines

Sanctis¹,

Oscarsson²,

Попов³

et al. 2016

Acta Cryst Sect D Struct Biol

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The constant evolution of synchrotron structural biology beamlines, the viability of screening protein crystals for a wide range of heavy-atom derivatives, the advent of efficient protein labelling and the availability of automatic dataprocessing and structure-solution pipelines have combined to make de novo structure solution in macromolecular crystallography a less arduous task. Nevertheless, the collection of diffraction data of sufficient quality for experimental phasing is still a difficult and crucial step. Here, some examples of good data-collection practice for projects requiring experimental phasing are presented and recent developments at the ESRF Structural Biology beamlines that have facilitated these are illustrated.

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JBluIce–EPICScontrol system for macromolecular crystallography

Cited by 47 publications

References 27 publications

Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV

Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV

Predicted optical performance of the GM/CA@APS micro-focus beamline

Facilitating best practices in collecting anomalous scattering data forde novostructure solution at the ESRF Structural Biology Beamlines

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