[ccp4bb] Research Fellow position at Nanyang Technological University

[Zhu Qiao]

A postdoc position (2 years at least, extendable) is immediately available in 
GYG’s lab, School of Biological Sciences (SBS), Nanyang Technological 
University (NTU), Singapore 
(https://dr.ntu.edu.sg/cris/rp/rp00878/selectedPublications.html). The 
successful applicant will be working on  protein quality control and RNA 
biology (RNA and its complex with protein functioning in viral infection and 
protein translation) through structural method in combination with biophysical 
& biochemical approaches. 

The lab is located in NISB (NTU Institute of Structural Biology) and SBS, where 
 state-of-the-art instruments, including EM facilities, are equipped for 
structural and biophysical investigation on protein and/or its 
complex with RNA(DNA). The lab is also clustered with a highly motivated and 
scientifically collaborated research groups. In addition, the lab currently is 
equipped with a good team who are working together for science as well as are 
staying together to grow up for a better life. 

Qualifications: Complete your PhD in structural biology, or biochemistry, or 
protein chemistry, or microbiology (virology).  The experience in structural 
biology, such as Cryo-EM or crystallography, would be beneficial. But if  you 
have good experience in recombinant protein preparation (molecular cloning, 
protein expression, and protein purification),  RNA /RNA-protein complex in 
vitro handling, as well as biophysical/biochemical characterization of protein 
and its complex, you are also encouraged to apply. 

Salary and benefit: We offer very competitive salary, and you will be covered 
by NTU employee benefit (such as medical insurance, annual year bonus etc). 
Please note that remuneration will definitely be commensurate with your 
experience and qualifications. 

Application: please submit a cover letter, your CV (including contact 
information for at least 2 references) to Dr Gao Yonggui (ygao(at)ntu.edu.sg, 
pls change “at’’ to “@”). Please note shortlisted candidates only will be 
notified). 



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[ccp4bb] CryoEM Current Practices Webinar This Thursday, 02/23/2023

[Christina Zimanyi]

Dear all,
Please join the NIH Transformative High Resolution CryoEM Program service 
centers this week at our CryoEM Current Practices webinar.

Time: Thursday, February 23, 2023 at 9 AM pacific / 12 PM eastern time
Speaker: Radhika Malik, PhD, Research Assistant Professor, Department of 
Pharmacological Sciences, Icahn School of Medicine at Mount Sinai

Title: Cryo-EM structures of DNA Polymerase Zeta in Translesion DNA Synthesis

All are welcome to attend. Registration is at no-cost, but sign-up is required:
https://us02web.zoom.us/webinar/register/WN_mjETzghsSaGL2QbDpYjhtA

Please forward this posting to anyone that may be interested.

Information about previous and future talks can be found at 
https://www.cryoemcenters.org/events/#cryoEM-webinar

Best regards,
National Center for CryoEM Access and Training



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Re: [ccp4bb] Unidentified density

[Lau Kelvin]

+++1 Glycerol
--
Kelvin Lau
Protein production and structure core facility - PTPSP
EPFL SV PTECH PTPSP
AI 2146 (Bâtiment AI)
Station 19
CH-1015 Lausanne
Switzerland
Email: kelvin@epfl.ch
Phone: +41 21 69 34494

On 21 Feb 2023, at 14:34, David Lawson (JIC) 
mailto:david.law...@jic.ac.uk>> wrote:

Hi Zeya,

Did you cryoprotect with glycerol perhaps?

Dave

---

Prof. David M. Lawson
Department of Biochemistry and Metabolism,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk


From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
On Behalf Of zeyaul islam
Sent: 21 February 2023 11:13
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unidentified density


You don't often get email from zeya1...@gmail.com. 
Learn why this is important

Dear all
 We have solved the structure of nanobody at 1.25 angstrom. We observe some 
unidentified density near the serine. Please have a look at the figures. 
Protein was purified in PBS buffer (137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 
2 mM KH2PO4) and the crystallisation condition has 0.1 M BIS-TRIS pH 5.5, 2.0 M 
ammonium sulfate. Any ideas what this could be? I tried SO4 and PO4 but didn’t 
satisfy the observed electron density.
I appreciate any help you can provide.
Thanks
Zeya
Zeyaul Islam, PhD
QBRI - Qatar Biomedical Research Institute
P.O. Box: 34110
Doha – Qatar
Tel: +974 445 46690




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Re: [ccp4bb] Unidentified density

[David Lawson (JIC)]

Hi Zeya,

Did you cryoprotect with glycerol perhaps?

Dave

---

Prof. David M. Lawson
Department of Biochemistry and Metabolism,
John Innes Centre,
Norwich,
NR4 7UH, UK.
Tel: +44-(0)1603-450725
Web: https://www.jic.ac.uk/people/david-lawson
Email: david.law...@jic.ac.uk


From: CCP4 bulletin board  On Behalf Of zeyaul islam
Sent: 21 February 2023 11:13
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unidentified density

You don't often get email from zeya1...@gmail.com. 
Learn why this is important
Dear all
 We have solved the structure of nanobody at 1.25 angstrom. We observe some 
unidentified density near the serine. Please have a look at the figures. 
Protein was purified in PBS buffer (137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 
2 mM KH2PO4) and the crystallisation condition has 0.1 M BIS-TRIS pH 5.5, 2.0 M 
ammonium sulfate. Any ideas what this could be? I tried SO4 and PO4 but didn’t 
satisfy the observed electron density.
I appreciate any help you can provide.
Thanks
Zeya
Zeyaul Islam, PhD
QBRI - Qatar Biomedical Research Institute
P.O. Box: 34110
Doha – Qatar
Tel: +974 445 46690




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[ccp4bb] Access to Diamond VMXi (room temperature beamline) via iNEXT

[Hough, Michael (DLSLtd,RAL,LSCI)]

Hi all,



We are now accepting applications for in situ plate-based data collection 
beamtime at VMXi, Diamond, for access through the 
iNEXT-Discovery project.



This access route provides funded access to Diamond for EU users. Existing 
users do not need to reapply but should contact VMXi staff for details 
regarding how to make an application for iNEXT-Discovery funding.



The deadline for proposals in the current submission period is Sunday 5th March.



VMXi offers a highly automated platform for obtaining room temperature crystal 
structures from crystals within their crystallisation plates. This allows for 
high quality room temperature structures to be straightforwardly determined and 
for crystal quality to be assessed without disturbance of the crystals via 
manual handling or cryoprotection. Currently MiteGen in situ and Greiner 
Crystal QuickX plates are accepted. Crystals may be identified using a machine 
learning tool or manually and the resulting multicrystal data are automatically 
merged using dials.multiplex.



Users via iNEXT may access the crystallisation facility at Harwell to set up 
crystallisation plates ready for data collection at VMXi.



Details of the crystallisation facility are available here:

https://www.diamond.ac.uk/Instruments/Mx/Crystallisation-Facility.html



A description of the beamline is shown here: 
https://www.diamond.ac.uk/Instruments/Mx/VMXi.html



For how to apply please see

https://www.diamond.ac.uk/Users/Support-for-European-Access-to-Life-Sciences/How-to-apply0.html



If you would like any further information or have questions, please contact me 
at michael.ho...@diamond.ac.uk

Thanks,

Mike


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are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
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Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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Re: [ccp4bb] Unidentified density

[Robbie Joosten]

This is always hard to see this way, but it looks like glycerol at first 
glance. Try to fit that.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of zeyaul
> islam
> Sent: Tuesday, February 21, 2023 12:13
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Unidentified density
> 
> Dear all
> 
>  We have solved the structure of nanobody at 1.25 angstrom. We observe some
> unidentified density near the serine. Please have a look at the figures. 
> Protein
> was purified in PBS buffer (137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2
> mM KH2PO4) and the crystallisation condition has 0.1 M BIS-TRIS pH 5.5, 2.0 M
> ammonium sulfate. Any ideas what this could be? I tried SO4 and PO4 but
> didn’t satisfy the observed electron density.
> 
> I appreciate any help you can provide.
> 
> Thanks
> 
> Zeya
> 
> Zeyaul Islam, PhD
> 
> QBRI - Qatar Biomedical Research Institute
> 
> P.O. Box: 34110
> Doha – Qatar
> 
> Tel: +974 445 46690
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




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[ccp4bb] ccp4 update 009

[Charles Ballard - STFC UKRI]

Dear All

A little late, but update to 8.0 009 is now available.

Brief description:

ccp4cloud -update to 1.7.010 
https://cloud.ccp4.ac.uk/manuals/html-userguide/jscofe_version_log.html

ccp4i2 - update to v2.0.  https://ccp4i2.gitlab.io/rstdocs/updatelog/index.html


cbuccaneerNN - new model building program


pairef - update to 1.3.
ccif - update to mmcif_pdbx_v50.dic

refmac - update to cif handling and bug fixes

pandda (on osx and linux) - further python3 fixes

monomers library - new monomers, BJ3, BQG, CZU, DJ5, G5F, G7C, I1X, K39, P3C, 
UQO, WEL, WJB, ZN1, correction FES


Details of earlier updates are available at CCP4 8.0 Updates - Collaborative 
Computational Project No. 4

CCP4 Core Team



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