[ccp4bb] MX Positions Available at EMBL Hamburg
Dear all, at EMBL Hamburg two positions are open in the MX-Team. We are looking for: - a Beamline Scientist in Macromolecular Crystallography https://www.embl.de/jobs/searchjobs/index.php?ref=HH_00108 - an Industrial Liaison Scientist in Macromolecular Crystallography https://www.embl.de/jobs/searchjobs/index.php?ref=HH_00112 For information about our beamlines: http://www.embl-hamburg.de/services/mx/ Best regards Thomas --- Dr. Thomas R. Schneider EMBL c/o DESY Notkestr. 85 22607 Hamburg Germany --- EMBL@Petra3: http://www.embl-hamburg.de/services/mx/ ORCID: http://orcid.org/-0001-6955-7374 ---
[ccp4bb] Postdoctoral Position Available to Study Structure and Mechanisms of Gene-regulatory Noncoding RNAs and Highly Structured Viral RNAs
A fully funded postdoctoral position (up to 5 years) is available in the Structural Biology of Noncoding RNAs and Ribonucleoproteins Section, Laboratory of Molecular Biology (LMB), NIDDK, in NIH’s vibrant main campus in Bethesda, MD near Washington DC. The lab addresses a widening gap between the accelerated discovery and functional description of the noncoding transcriptome, and a paucity of 3D structures and mechanistic understanding of complex noncoding RNAs. We seek a new member to join our diverse group to deepen current work on gene-regulatory riboswitches, highly structured viral RNAs, circular and other structured long noncoding RNAs. https://www-mslmb.niddk.nih.gov/zhang/zhanglab.html Current manuscripts and recent publications: 1. Li et al., & Zhang (2017) Structural basis of amino acid sensing on the tRNA by a T-box riboswitch. In preparation. 2. Bahmanjah et al., & Zhang (2017) Structural basis of functional repurposing of an aminoacyl-tRNA synthetase in stress response. In preparation. 3. Hood et al., & Zhang (2017) Structural mimicry of codon-anticodon interactions by a viral noncoding RNA. In preparation. 4. Zhang & Ferré-D'Amaré (2014) Dramatic improvement of crystals of large RNA by cation replacement and dehydration. Structure 22, 1363-1371. 5. Zhang & Ferré-D'Amaré (2014) Direct evaluation of tRNA aminoacylation status by the T-box riboswitch using tRNA-mRNA stacking and steric readout. Molecular Cell 55, 148-155. 6. Zhang & Ferré-D'Amaré (2013) Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature 500, 363-7. The lab is part of the Earl Stadtman Investigator program for high-risk, high-impact research at the NIH intramural program consisting of 1100 labs. The well-supported lab has dedicated access to state-of-the-art equipment in structural biology (Mosquito, Dragonfly, Rock Imager, Akta Pures, FSEC, for X-ray crystallography; new Titan Krios for single-particle Cryo-EM; SAXS, AFM, etc), efficient biochemistry, biophysics (ITC, DSC, SPR, BLI, AUC, DLS, SEC-MALS, CD, fluorescence, thermophoresis, etc), fermentation, genomics, and proteomics core facilities with hands-on training or service by PhD-level staff scientists. The NIH, NIDDK, and LMB are committed to the continued education and career development of trainees through numerous courses and workshops offered by NIH OITE and FAES. Requirements: Interested candidates must have received (or be expecting) a Ph.D. or M.D. within the past five years in molecular or structural biology, biochemistry, or biophysics, and be strongly self-motivated to lead innovative and rigorous research projects. Strong background in protein expression and purification, enzyme kinetics, and structural biology is desirable. To apply: Please email a preferred start date, CV, a brief summary of research interests, accomplishments, and career goals, and names and contact information for at least three references to: Dr. Jinwei Zhang, Email: jinwei.zh...@nih.gov. The NIH is dedicated to building a diverse community and DHHS/NIH is an Equal Opportunity Employer.
Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] B-factors/Occupancies Versus "Local Resolution"
Hi Ian, and thanks for the interesting email.
The insect example should be understood in the context of the OED definition of
resolution, which uses the word “measureable.” If one has a megapixel image of
a blurred-wing insect, the wings are certainly “measureable” in principle, but
are in reality—in their nature—blurry. This is because, as you pointed out, the
time-resolution is not good enough. The spatial resolution, however, is
certainly good enough. I would think, therefore, that it is somewhat misleading
to estimate the resolution of the image based on not being able to see the
wings.
That example, however, is perhaps not the best, since it’s complicated by
involving time.
A simpler example, perhaps, would be of something which is inherently blurry
even at one instant, say a protein diffracting in crystalline form. Since the
structure is averaged over many unit cells, the average structure is inherently
blurry in different places (especially in bulk sovent!), which is what the
ADPs/occ’s model. Even if I had a radiation-proof crystal with infinitesimal
mosaicity, and could see spots at 0.5 angstroms, the blurry parts would remain
blurry, even though the resolving power of the experiment would certainly imply
being able to distinguish atoms.
Perhaps an even more plain example: image a megapixel image of a
completely-white featureless surface. I cannot see anything distinct in the
image, but I know that if there were two black dots of a certain spatial
separation, I would be able to distinguish them. If there are actually no dots,
does that mean my resolution is nil? Or if there were dots, does it make sense
to say that the local resolution around the dots be vastly better than in the
blank parts? I don’t think so.
Therefore I favor thinking of resolution in this conditional sense: under the
current imaging setup, what separations would I be able to distinguish, if
there were ideal features there to image?
The cryo-EM definition of local resolution does not seem to fit this
definition, and I remain unsure why they use this metric. Perhaps I will do a
little reading and talk to some experts around here.
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle
Sent: Tuesday, March 07, 2017 10:27 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] B-factors/Occupancies Versus
"Local Resolution"
Hi Yong
Yes of course the _average_ resolution of the map, whether from single crystal
or PD, is determined 'more or less' by the minimum d-spacing ('resolution
limit'), in the same way that the _average_ quality of the agreement between
the model and the data is related 'more or less' to the R factor, but is that
good enough? It tells you nothing at all about how the resolution or the
quality of fit of the model varies spatially over the map. Also d_min need not
be a single number as is traditionally claimed in the vast majority of
literature articles: there's no reason at all why it shouldn't be anisotropic
(varying with direction), though even this doesn't tell you about the
resolution as a function of position in the map.
Yes the resolution of the Patterson map obviously won't depend on the model,
but how often is the Patterson resolution useful in practice? I think normally
the width of the origin peak is more useful. I would say the resolution of the
ED or EM map is what interests most people.
My point about the difference between the meaning of resolution as used in
single-crystal MX compared with other fields is that MX is the only field AFAIK
where 'resolution' is frequently used in the way it is, i.e. as a reciprocal
space property of individual reflexions. We already had for many years (in
fact since Bragg proposed his famous law!) the concept of d-spacing and d_min.
In all other disciplines that use imaging, resolution is a property of the
image (which could of course be a diffraction image), period. Using the same
word with two different meanings only confuses people, particularly when we
already had a perfectly good word!
Cheers
-- Ian
On 7 March 2017 at 14:49, Yong Wang
mailto:wang_yon...@lilly.com>> wrote:
Ian,
Won’t the spatial resolution of the electron density map be determined more or
less by the “resolution” (d-spacing)? While the normal electron density
includes model contribution, what about the resolution of the Patterson map?
For the case of powder diffraction, after the lines are resolved, won’t the
spatial resolution of the Fourier synthesis still depend on the d-spacing
resolution limit? I don’t see much difference of the resolution used in
crystallography from those used in other fields.
Cheers,
Yong
From: CCP4 bulletin board
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian
Tickle
Sent: Tuesday, March 07, 2017 9:02 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] Re: [ccp4bb] B-factors/Occupancies V
Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] B-factors/Occupancies Versus "Local Resolution"
Hi Yong
Yes of course the _average_ resolution of the map, whether from single
crystal or PD, is determined 'more or less' by the minimum d-spacing
('resolution limit'), in the same way that the _average_ quality of the
agreement between the model and the data is related 'more or less' to the R
factor, but is that good enough? It tells you nothing at all about how the
resolution or the quality of fit of the model varies spatially over the
map. Also d_min need not be a single number as is traditionally claimed in
the vast majority of literature articles: there's no reason at all why it
shouldn't be anisotropic (varying with direction), though even this doesn't
tell you about the resolution as a function of position in the map.
Yes the resolution of the Patterson map obviously won't depend on the
model, but how often is the Patterson resolution useful in practice? I
think normally the width of the origin peak is more useful. I would say
the resolution of the ED or EM map is what interests most people.
My point about the difference between the meaning of resolution as used in
single-crystal MX compared with other fields is that MX is the only field
AFAIK where 'resolution' is frequently used in the way it is, i.e. as a
reciprocal space property of individual reflexions. We already had for
many years (in fact since Bragg proposed his famous law!) the concept of
d-spacing and d_min. In all other disciplines that use imaging, resolution
is a property of the image (which could of course be a diffraction image),
period. Using the same word with two different meanings only confuses
people, particularly when we already had a perfectly good word!
Cheers
-- Ian
On 7 March 2017 at 14:49, Yong Wang wrote:
> Ian,
>
>
>
> Won’t the spatial resolution of the electron density map be determined
> more or less by the “resolution” (d-spacing)? While the normal electron
> density includes model contribution, what about the resolution of the
> Patterson map? For the case of powder diffraction, after the lines are
> resolved, won’t the spatial resolution of the Fourier synthesis still
> depend on the d-spacing resolution limit? I don’t see much difference of
> the resolution used in crystallography from those used in other fields.
>
>
>
> Cheers,
>
>
>
> Yong
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Ian
> Tickle
> *Sent:* Tuesday, March 07, 2017 9:02 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [EXTERNAL] Re: [ccp4bb] B-factors/Occupancies Versus "Local
> Resolution"
>
>
>
>
>
> Hi Jacob
>
> I'm a bit puzzled that you say that what you call 'local resolution' is
> used 'to model disordered regions' in cryo-EM. AFAIK it does no such
> thing: resolution is certainly used as a _metric_ of the EM map quality but
> it's not used for modelling. High resolution EM maps (which I assume is
> what we are talking about) are modelled in exactly the same way as X-ray
> maps, i.e. using an atomic model with co-ordinates, occupancies and B
> factors. Also I don't understand what you are saying about the insect
> wings: if they are blurred how can you 'see the wings' the same as you
> would stationary wings?, i.e. how can they have the same resolution as
> stationary wings, unless of course you change the experiment and stop the
> motion somehow (e.g. by using high-speed photography, but then note that
> greatly reducing the exposure time per image will also reduce the
> signal/noise ratio).
>
> Blurring (aka thermal motion or disorder) means 'loss of resolution',
> since if objects are moving or disordered the distance at which they can be
> distinguished as separate will clearly increase. So places in an electron
> density or EM map where atoms have moved over the exposure time of the
> experiment or are disordered (positioned differently in different unit
> cells or particles used in the averaging) will vary in resolution. This
> suggests that it might indeed be useful to analyse the variation of
> resolution in ED maps as is done in EM maps.
>
>
> I think part of the problem is that there's a good deal of confusion
> amongst MX practitioners in particular over the meaning of 'resolution'.
> The OED at least is very clear what it means: 'The smallest interval
> measurable by a telescope or other scientific instrument; the resolving
> power.'. This is precisely what it means in the overwhelming majority of
> scientific disciplines that make use of imaging (astronomy, EM, seisomology
> etc), and is also the definition you will find in all textbooks on optics
> and imaging in general.
>
> However macromolecular crystallography seems to be the one exception,
> where for example the descriptor 'resolution' in the MX literature is
> frequently ascribed to individal X-ray reflexions when what is meant is
> 'd-spacing' (or something directly related to that such as the magnitude of
> the scattering vector d*). This makes absolutely no sense! - resolution is
> the property of an _imag
Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] B-factors/Occupancies Versus "Local Resolution"
Ian, Won’t the spatial resolution of the electron density map be determined more or less by the “resolution” (d-spacing)? While the normal electron density includes model contribution, what about the resolution of the Patterson map? For the case of powder diffraction, after the lines are resolved, won’t the spatial resolution of the Fourier synthesis still depend on the d-spacing resolution limit? I don’t see much difference of the resolution used in crystallography from those used in other fields. Cheers, Yong From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent: Tuesday, March 07, 2017 9:02 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] Re: [ccp4bb] B-factors/Occupancies Versus "Local Resolution" Hi Jacob I'm a bit puzzled that you say that what you call 'local resolution' is used 'to model disordered regions' in cryo-EM. AFAIK it does no such thing: resolution is certainly used as a _metric_ of the EM map quality but it's not used for modelling. High resolution EM maps (which I assume is what we are talking about) are modelled in exactly the same way as X-ray maps, i.e. using an atomic model with co-ordinates, occupancies and B factors. Also I don't understand what you are saying about the insect wings: if they are blurred how can you 'see the wings' the same as you would stationary wings?, i.e. how can they have the same resolution as stationary wings, unless of course you change the experiment and stop the motion somehow (e.g. by using high-speed photography, but then note that greatly reducing the exposure time per image will also reduce the signal/noise ratio). Blurring (aka thermal motion or disorder) means 'loss of resolution', since if objects are moving or disordered the distance at which they can be distinguished as separate will clearly increase. So places in an electron density or EM map where atoms have moved over the exposure time of the experiment or are disordered (positioned differently in different unit cells or particles used in the averaging) will vary in resolution. This suggests that it might indeed be useful to analyse the variation of resolution in ED maps as is done in EM maps. I think part of the problem is that there's a good deal of confusion amongst MX practitioners in particular over the meaning of 'resolution'. The OED at least is very clear what it means: 'The smallest interval measurable by a telescope or other scientific instrument; the resolving power.'. This is precisely what it means in the overwhelming majority of scientific disciplines that make use of imaging (astronomy, EM, seisomology etc), and is also the definition you will find in all textbooks on optics and imaging in general. However macromolecular crystallography seems to be the one exception, where for example the descriptor 'resolution' in the MX literature is frequently ascribed to individal X-ray reflexions when what is meant is 'd-spacing' (or something directly related to that such as the magnitude of the scattering vector d*). This makes absolutely no sense! - resolution is the property of an _image_, which in the case of MX means the electron density map (or electric potential map in cryo-EM). This means that X-ray resolution depends on the model as well as the data, since the resolution is a property of the ED map, the map depends on the amplitudes and phases, the amplitudes depend on the data and the phases depend on the model. The situation is of course different in cryo-EM where the map is obtained directly from the data (which effectively contains both amplitude and phase information), so unlike the situation with X-ray maps, EM resolution has no dependence on the model. If resolution means anything in an X-ray diffraction pattern, it means the minimum distance on the detector between adjacent spots at which the spots are seen as separate, i.e. no spot overlap. This is in fact precisely the (correct) meaning that is routinely used in powder diffraction (http://www.ccp14.ac.uk/solution/resolution_powder_diffraction.html), i.e. the minimum separation of lines in the pattern that can be distinguished; it has nothing whatever to do with the minimum d-spacing of the lines in the pattern. There's really no good reason for MX to be so out of line with all other imaging techniques in this regard! Note that the accepted definition implies that resolution may be a function of position, so there is no reason in general to believe that it will have the same value everywhere even in a single image, so we should not make that assumption either explicitly or implicitly. The single-valued 'resolution limit' (minimum d-spacing), derived from the data immediately after processing and which is always quoted in the literature, is only an estimate of the average resolution, much like the R factor is an estimate of the average overall agreement between the data and the model, which tells you nothing
Re: [ccp4bb] B-factors/Occupancies Versus "Local Resolution"
Hi Jacob I'm a bit puzzled that you say that what you call 'local resolution' is used 'to model disordered regions' in cryo-EM. AFAIK it does no such thing: resolution is certainly used as a _metric_ of the EM map quality but it's not used for modelling. High resolution EM maps (which I assume is what we are talking about) are modelled in exactly the same way as X-ray maps, i.e. using an atomic model with co-ordinates, occupancies and B factors. Also I don't understand what you are saying about the insect wings: if they are blurred how can you 'see the wings' the same as you would stationary wings?, i.e. how can they have the same resolution as stationary wings, unless of course you change the experiment and stop the motion somehow (e.g. by using high-speed photography, but then note that greatly reducing the exposure time per image will also reduce the signal/noise ratio). Blurring (aka thermal motion or disorder) means 'loss of resolution', since if objects are moving or disordered the distance at which they can be distinguished as separate will clearly increase. So places in an electron density or EM map where atoms have moved over the exposure time of the experiment or are disordered (positioned differently in different unit cells or particles used in the averaging) will vary in resolution. This suggests that it might indeed be useful to analyse the variation of resolution in ED maps as is done in EM maps. I think part of the problem is that there's a good deal of confusion amongst MX practitioners in particular over the meaning of 'resolution'. The OED at least is very clear what it means: 'The smallest interval measurable by a telescope or other scientific instrument; the resolving power.'. This is precisely what it means in the overwhelming majority of scientific disciplines that make use of imaging (astronomy, EM, seisomology etc), and is also the definition you will find in all textbooks on optics and imaging in general. However macromolecular crystallography seems to be the one exception, where for example the descriptor 'resolution' in the MX literature is frequently ascribed to individal X-ray reflexions when what is meant is 'd-spacing' (or something directly related to that such as the magnitude of the scattering vector d*). This makes absolutely no sense! - resolution is the property of an _image_, which in the case of MX means the electron density map (or electric potential map in cryo-EM). This means that X-ray resolution depends on the model as well as the data, since the resolution is a property of the ED map, the map depends on the amplitudes and phases, the amplitudes depend on the data and the phases depend on the model. The situation is of course different in cryo-EM where the map is obtained directly from the data (which effectively contains both amplitude and phase information), so unlike the situation with X-ray maps, EM resolution has no dependence on the model. If resolution means anything in an X-ray diffraction pattern, it means the minimum distance on the detector between adjacent spots at which the spots are seen as separate, i.e. no spot overlap. This is in fact precisely the (correct) meaning that is routinely used in powder diffraction ( http://www.ccp14.ac.uk/solution/resolution_powder_diffraction.html), i.e. the minimum separation of lines in the pattern that can be distinguished; it has nothing whatever to do with the minimum d-spacing of the lines in the pattern. There's really no good reason for MX to be so out of line with all other imaging techniques in this regard! Note that the accepted definition implies that resolution may be a function of position, so there is no reason in general to believe that it will have the same value everywhere even in a single image, so we should not make that assumption either explicitly or implicitly. The single-valued 'resolution limit' (minimum d-spacing), derived from the data immediately after processing and which is always quoted in the literature, is only an estimate of the average resolution, much like the R factor is an estimate of the average overall agreement between the data and the model, which tells you nothing about the magnitude of departures from the average. You need to look at the local metrics of agreement between the model and the electron density to get the full picture of the variation: similarly you need to look at the map to get the full picture of the variation of resolution. You can of course go to a multi-valued resolution limit, e.g. 6 parameters to describe it with an ellipsoid, or many parameters to describe it in terms of a fully general anisotropic surface. However this still does not address the fundamental problem that the resolution is a property of an image (map) which can vary with position in that image. Just my 2p's worth! Cheers -- Ian On 6 March 2017 at 19:54, Keller, Jacob wrote: > Dear Crystallographers (and cryo-EM practitioners,) > > > > I do not understand wh
Re: [ccp4bb] Crystallization suggestion for antigen-Fc complex
Ankita, Fc are different from Fabs. Even if glycosylated their solubility is lower. Fc stands for constant fragment but also for Fragment crystallizable: https://en.wikipedia.org/wiki/Fragment_crystallizable_region From its name, they should be easy to crystallize. If you have problems to not hesitate to ask questions. Enrico. On Tue, 07 Mar 2017 07:14:34 +0100, Ankita Srivastava wrote: Dear CCP4 members, I am trying to crystallize an antigen-bound to the Fc fragment of an antibody. Is Fc fragment difficult to crystallize compared to Fab? Are there any commercial screens widely known to crystallize Fc fragment or antibodies? I would appreciate if you can share any experience with crystallizing Fc fragment or Fc-complex with other proteins. Many thanks in advance! Ankita -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71 Proxima-2A, Soleil Synchrotron. Tel: 33 (0)1 69 35 8180 Beamline http://scholar.google.com/citations?hl=en&user=Kvm06WIoPAsC&pagesize=100&sortby=pubdate
[ccp4bb] Cryo-EM Symposium, 6-7 July 2017, European Photon & Neutron Campus, Grenoble, France
Dear all, We are pleased to announce the Cryo-Electron Microscopy Symposium that will take place from 6-7th July, 2017 in Grenoble, France. The aim of this symposium is to promote the exciting opportunities in structural biology opened by the advances in cryo-electron microscopy and by the integration of structural biology approaches at multi-resolution level. This symposium will celebrate the establishment of a new cryo-EM platform on the EPN campus. The platform will offer access to the international structural biology community to a new Titan Krios equipped with a Quantum LS filter and phase plate. Such microscope will be installed as a user facility at the ESRF and will reinforce the ongoing EM activity at the IBS and at the EMBL. The new facility will thus be open to the user community based on peer-review of scientific merit and technical feasibility. Scientists from ESRF, IBS and EMBL will support user operation. The symposium will bring together leading experts, junior researchers and representatives of industrial partners to present and discuss the latest developments and the future trends in cryo-EM as well as their applications in addressing biological challenges. It will also provide a forum for discussion among both established and junior scientists from different disciplines. We encourage participants to present their scientific results in a poster session, with the possibility of being selected for a short talk. Due to limited attendance (maximum of 80 external participants), early registration is encouraged. More information can be found at: http://www.esrf.fr/cryo-em.fr We look forward to seeing you in Grenoble! On behalf of the Organising committee: Stephen Cusack (EMBL), Trevor Forsyth (ILL/Keele), Wojciech Galej (EMBL), Gordon Leonard (ESRF), Marco Marcia (EMBL), Christoph Mueller-Dieckmann (ESRF), Hugues Nury (IBS), Guy Schoehn (IBS), Montserrat Soler-Lopez (ESRF), Jean Susini (ESRF) and Winfried Weissenhorn (IBS). -- MontseSOLER LOPEZ, PhD European Synchrotron Radiation Facility Structural Biology Group Carl-Ivar Branden Building - office 114 71 Avenue des Martyrs – CS 40220 F-38043 Grenoble Cedex 09 Phone: +33 (0)47688 1770 Fax:+33 (0)47620 9400
[ccp4bb] Postdoc position @ AstraZeneca, Sweden
Dear all, We're looking for a talented scientist to join the AstraZeneca Post Doc Programme to study the structure and function of a full-length transcription factor in complex with novel ligands and link this information to broader mode of action studies for active clinical projects. You will work in a highly dynamic environment with input from many different functions across the company. For full details about the position, requirements and how to apply, please follow the link below. Best regards Karl Edman https://job-search.astrazeneca.com/job/gothenburg/postdoc-fellow-structure-and-biophysics-gothenburg-sweden/7684/4031185 Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.
