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Time-resolved macromolecular serial crystallography – Course and Conference Office

EMBO Practical Course

Time-resolved macromolecular serial crystallography

Overview

Course overview

The advent of serial crystallography at free electron laser sources and the following adaptation of these methods at 3rd and 4th generation synchrotrons have opened new possibilities to perform room temperature time resolved studies in macromolecular crystallography.

This course aims to train the next generation of researchers in

i) sample preparation: Participants will be trained and taught in the best practice to obtain homogenous microcrystals and in characterisation prior to loading using different sample delivery methods,

ii) crystal delivery methods and data collection at a 4th generation synchrotron serial crystallography beamline: The new ID29 and similar endstations at other sources, presents experimental setup and data collection protocols that are unique in the synchrotron facilities. The training will include data collections with different sample delivery methods as available to the user community,


iii) data reduction: Diffraction data are recorded from still microcrystals with large bandwidth high flux X-ray beams which requires the use of specifically developed and adapted software.


iv) analysis of the electron density map differences: To correctly interpret and model the electron density differences map to highlight structural changes induced by pump-probe and ligand mixing experiments.

Audience

The course is aimed at advanced PhD students and early-career scientists, working in X-ray crystallography, who have prior acquaintance of serial crystallography and willing to pursue projects requiring enzymatic reaction studies. Moreover, participants should clearly provide or show a direct intent of applying time-resolved serial crystallography to their research projects. In selecting participants, we look for scientific merits in presenting their motivation, immediate application of the methods learned, strong background in understanding various aspects of crystallography basics and of studying enzymatic reactions. As the course is to introduce participants to the forefront of structural biology, big data analysis will be extensively carried out. This would require background in basic programming or ability to use Linux command lines.

Modules/Resources

  • Micro-crystallization strategies for – soluble and membrane proteins
  • Time-resolved in-crystallo spectroscopy to study reaction kinetics
  • Tricks to run an injector-based sample delivery for serial crystallography experiments
  • Fixed-target serial crystallography experiments
  • Hands-on experience on serial crystallography measurement at ID29 beamline
  • Serial crystallography data analysis using latest softwares
  • Time-resolved data interpretation using real-life cases

Learning Outcomes

Participants should be able to apply what they have learnt to their own projects. For each module, the participants will learn the theoretical and practical aspects of latest developments in the field. After the course, they will confidently be able to conduct a time-resolved experiment to study enzymatic reactions

Speakers and trainers

James Beilsten-Edmunds

DLS, Didcot

UK

Alexandra Tolstikova

DESY, CFEL Hamburg

Germany

Scientific organisers

Course organisers

Tracey Culloty

EMBL Grenoble

France

Sophie Dutzi

EMBL Heidelberg

Germany

Irena Provaznikova

EMBL Heidelberg

Germany

Claudine Romero

ESRF

France

Preliminary programme

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  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) with estimated time 0-10 hours will be required and will be shared in advance of the course.
  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.

Please note the below programme is still subject to changes

Day 1 – Monday 8 July 2024
Time (Europe/Berlin)Session
09:00 – 10:00Registration and Welcome coffee
10:00 – 10:10Welcome and course introduction
10:10 – 12:00Participants introduction / Flash Talks
12:00 – 13:30Lunch at EPN Canteen
14:00 – 14:45Lecture 1: Keynote
Petra Fromme – Arizona State University, USA
14:45 – 15:00Q&A discussion
15:00 – 15:20Lecture 2: Introduction to beamlines for serial crystallography
Daniele de Sanctis – ESRF, France
15:20 – 15:30Q&A discussion
15:30 – 16:00Coffee break
16:00 – 16:20Lecture 3: Overview on X-ray detector technology
Sofia Trampari – Dectris, Switzerland
16:20 – 16:30Q&A discussion
16:30 – 19:00Poster Presentation
19:00 – 20:00Dinner
20:00 – 21:00Discussion on FAIR Practice
21:00 Departure to Hotel
Day 2 – Tuesday 9 July 2024
Time (Europe/Berlin)Session
09:00 – 09:05Sample Preparation
09:05 – 09:25Lecture 4: Crystal quality/homogeneity/density – what is a good sample?
Ashwin Chari – Max-Planck Institute, Gottingen, Germany
09:25 – 09:30Q&A discussion
09:30 – 09:50Lecture 5: How to grow microcrystals
John Beale – Paul Scherrer Institute, Switzerland
09:50 – 09:55Q&A discussion
09:55 – 10:25Coffee break
10:25 – 10:45Lecture 6: LCP crystallization
Chia-Ying Huang – Swiss Light Source (SLS) Paul Scherrer Institute, Switzerland
10:45 – 10:50Q&A discussion
10:50 – 11:10Lecture 7: In vivo crystallization
Lars Redecke – University of Lubeck, Germany
11:10 – 11:15Q&A discussion
11:15 – 11:35Lecture 8: Microcrystallization in anaerobic condition
Yvain Nicolet – IBS Grenoble, France
11:35 – 11:40Q&A discussion
11:40 – 12:00Lecture 9: TR-icOS spectroscopy
Antoine Royant – IBS, Grenoble, France
12:00 – 12:10Q&A discussion
12:10 – 13:30Lunch
13:30 – 16:00Practical Session 1
Lead tutors: Dr. Monika Spano, Dr. Jose Martin Garcia, Dr. Antoine Royant, Dr. Sylvain Engilberge, Dr. Yvain Nicolet and Dr. Chia-Ying Huang
16:00 – 16:30Coffee break
16:30 – 19:00Practical Session 1 continued
Lead tutors: Dr. Monika Spano, Dr. Jose Martin Garcia, Dr. Antoine Royant, Dr. Sylvain Engilberge, Dr. Yvain Nicolet and Dr. Chia-Ying Huang
19:00 – 20:30Dinner
20:30Departure to Hotel
Day 3 – Wednesday 10 July 2024
Time (Europe/Berlin)Session
09:00 – 09:05Sample delivery and data collection
09:05 – 09:25Lecture 10: Delivery using injectors
Anastasya Shilova – DLS, Didcot, UK
09:25 – 09:30Q&A discussion
09:30 – 09:50Lecture 11: Delivery using fixed target, tape-drive, acoustic levitator
Pedram Mehrabi – UHH Hamburg, Germany
09:50 – 09:55Q&A discussion
09:55 – 10:25Coffee break
10:25 – 10:45Lecture 12: Mixing and microfluidics
Alexandra Ros – Arizona State University, USA
10:45 – 10:50Q&A discussion
10:50 – 11:10Lecture 13: Best practice for serial data collection
Arwen Pearson – CFEL Hamburg, Germany
11:10 – 11:15Q&A discussion
11:15 – 11:35Lecture 14: Laser activation for time-resolved experiments
Wiktor Szymanski – University of Groningen, Netherlands
11:35 – 11:40Q&A discussion
11:40 – 12:00Lecture 15: Pink beam time-resolved serial crystallography
Alexandra Tolstikova – DESY, CFEL Hamburg, Germany
12:00 – 12:10Q&A discussion
12:10 – 13:30Lunch
13:30 – 16:00Practical Session 2
Lead tutors: Dr. Julien Orlans, Dr. Oskar Aurelius, Dr. Daniele de Sanctis, Dr. Shibom Basu, Dr. Pedram Mehrabi
16:00 – 16:30Coffee break
16:30 – 19:00Practical Session 2 continued
Lead tutors: Dr. Julien Orlans, Dr. Oskar Aurelius, Dr. Daniele de Sanctis, Dr. Shibom Basu, Dr. Pedram Mehrabi
19:00 – 21:00Dinner and drinks
21:00Departure to Hotel
Day 4 – Thursday 11 July 2024
Time (Europe/Berlin)Session
09:00 – 09:05Session Overview: Serial crystallography data processing
09:05 – 09:25Lecture 16: Serial crystallography theory and statistics/data quality
Nadia Zatsepin – La Trobe University, Melbourne, Australia
09:25 – 09:30Q&A discussion
09:30 – 09:50Lecture 17: CrystFEL – best practice
Thomas White – DESY, CFEL Hamburg, Germany
09:50 – 09:55Q&A discussion
09:55 – 10:25Coffee break
10:25 – 10:45Lecture 18: Dials / cctbx.xfel
James Beilsten-Edmands – DLS, Didcot, UK
10:45 – 10:50Q&A discussion
10:50 – 11:10Lecture 19: Interpretation and calculation of difference maps, refinements – time-resolved data
Elke de Zitter – IBS Grenoble, France
11:10 – 11:15Q&A discussion
11:15 – 11:50Lecture 20: Paying attention to radiation damage in serial data
Elspeth Garman – University of Oxford, UK
11:50 – 12:00Q&A discussion
12:00 – 13:30Carreer Lunch with PSB scientists
13:30 – 15:30Practical Session 3
Dr. Thomas White, Dr. James Beilstain-Edmands
and Dr. Elke de Zitter
15:30 – 16:00Coffee break
16:00 – 19:00Practical Session 3 continued
Dr. Thomas White, Dr. James Beilstain-Edmands
and Dr. Elke de Zitter
19:00 – tbcGala Dinner
tbcDeparture to Hotel
Day 5 – Friday 12 July 2024
Time (Europe/Berlin)Session
09:00 – 09:05Session Overview: Group Activity
09:05 – 11:00Brainstorming: Participant Groups will work on ideas to do new experiments at the beamline
11:00 – 11:10Presentation Group 1
11:10 – 11:20Presentation Group 2
11:20 – 11:30Presentation Group 3
11:30 – 11:40Presentation Group 4
11:40 – 12:10Coffee break
12:10 – 12:30Course Evaluation
12:30 – 13:00Closing Remark
13:00 – 13:30Lunch and Departure

Practical information

Registration fees and motivation letter

The course is limited to 20 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration

Registration fees include accommodation (location TBC), all meals throughout the duration of the course, admission and course materials. Travel expenses are NOT covered with the registration fee.

Academia€425
PhD Student€425
Industry€1000

A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed. We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.

Confirmation and payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation letter submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.

Instructions

  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

  • The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
  • If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
  • If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For detailed instructions, please watch our video on how to submit a course motivation letter.

Further details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial assistance

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of registration fee waiverstravel grants and childcare grants

Your place in the meeting is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:

– up to €400 for participants travelling to an EMBL Course within Europe.

– up to €1000 for participants travelling to an EMBL Course from outside Europe.

– up to €500 for any participant travelling to an EMBO Practical Course.

– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.

– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.

*Registration fees are only covered for EMBO Practical Courses

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Childcare grant

There is the possibility to apply for a childcare grant to offset child care costs incurred by participants, speakers, trainers and organisers when attending a course. Eligible costs include (but are not limited to) fees for a babysitter or child-care facility and travel costs for a caregiver. Please note that priority will be given to early-stage researchers. There is a limited amount of funding available for the childcare grants and funds will be distributed amongst eligible applicants.

Boehringer Ingelheim Fonds travel grant

Applies to selected courses only. Availability will be indicated during the motivation letter submission process.

This grant covers costs related to your attendance at the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.

Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course

– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course

Application

You may apply for financial assistance when submitting your motivation letter for courses. In your application, you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

For the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.

Selection

The scientific organisers will select the recipients of registration fee waivers and travel grants during the motivation letter or abstract selection process. Results will be announced approximately 6 – 8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the meeting. Selection for registration fee waivers and travel grants is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.

Childcare grants will be allocated in the same timeframe (6-8 weeks before the event start date). Please note that priority will be given to early-stage researchers.

Reimbursement

Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.

Accomodation and shuttles

Hotel

Reservations have been made for course participants at accommodation at the guesthouse located in the EPN campus which hosts the EMBL Grenoble site More details will be available soon. Note, accommodation is included in the registration fee. 

Local transport

Shuttle buses will go from the Hotel to the EMBL campus and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Further details

Address: EMBL Grenoble, 71 Av. des Martyrs, 38000 Grenoble, France

From Lyon-Saint Exupéry Airport take the airport shuttle bus Lyon-Saint Exupéry–Grenoble counter (Satobus) inside the airport or in the bus. A single ticket costs 22€, a return ticket 33€.The stop “Place de la Résistance” is within easy walking distance of the EMBL site.

From Grenoble take Tram B towards “Resistance roundabout” and exit at “Grenoble Presquile”. The site entry is 350m away from the stop.

For further information on getting to EMBL Grenoble visit our Travel Information page.

Technical requirements and event software

Technical requirements

Information will be provided ahead of the course about installing any software required.

Event software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

At the mandatory on-boarding session on Wednesday, 5 June the functionalities of the platform and course content will be further explained.

Technical requirements

All participants must bring their own laptops

COVID-19 related questions

Updated information will be provided closer to the time  of the on-site module.

Sponsors

Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other events, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

Warning

EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.

Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

Media kit

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Date: 8 - 12 Jul 2024

Location: EMBL Grenoble

Venue: EPN Campus, Grenoble


Deadline(s):

Application: 15 Apr 2024


Organisers:

  • Oskar Aurelius
    MAX IV Laboratory, Sweden
    • Shibom Basu
      EMBL Grenoble, France
      • Gisela Brändén
        University of Gothenburg, Sweden

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