XXV IUCr Satellite Workshop: Methods of Structural Biology

Joining CCP4/CCP-EM online workshop and CMS workshop

Dates: August 9 – 10, 2021 (CCP4/CCP-EM), August 12 – 13, 2021 (CMS)

Venue: Online + Institute of Biotechnology of the Czech Academy of Sciences, Biocev Centre, Vestec near Prague

Aim:   The CMS workshop will provide training and hands on experience in selected structural biology techniques available at the Centre of Molecular Structure (CMS) at IBT. Introductory talks will be accompanied by more advanced insights into biophysics, protein crystallization, X-ray diffraction, small angle X-ray scattering and structural mass spectrometry. Sessions at instruments will focus on training in selected techniques.

            The CCP4/CCP-EM online workshop will focus on theory and practice in computational approaches in bio-crystallography and Cryo-EM single particle analysis.

Format: The CCP4/CCP-EM workshop will be organized online by the CCP4 and CCP-EM staff. The CMS workshop, organized by the CMS staff, will be on site. According to the epidemiological situation, we will confirm this format or announce changes.
There is a one-day break – August 11 – for travel of those who want to participate in both workshops.

Participation fee:

CCP4/CCP-EM – free.
CMS workshop - 150 EUR (meals and course materials; does not cover accommodation and dinner on 11 Aug)

To apply: Please fill out the preliminary registration from both parts HERE. You can register to one or both workshops. In the case of high interest, preference will be given to those registered to both workshops. You will receive confirmation (and payment details if applicable) before the end of June.

Application deadline: The deadline for preliminary registration is June 17, 2021. The payment deadline is July 31, 2021.

Contact to organizers:

Jan Dohnálek (CMS) – dohnalek at ibt.cas.cz
Magdalena Schneiderová (CMS) - magdalena.schneiderova at ibt.cas.cz
Jan Stránský (CMS) – jan.stransky at ibt.cas.cz
CCP4/CCP-EM - ccp4 -at- stfc.ac.uk

CCP4/CCP-EM online workshop

Monday, August 9

09:00-09:45 CCP4 Cloud Setup and General Introduction
09:45-10:45 Data processing and reduction
10:45-11:00 Break
11:00-12:00 Experimental Phasing and Density Modification
12:00-13:00 Lunch break
13:00-13:45 Molecular Replacement
13:45-14:45 Model Building and Refinement
14:45-15:00 Break
15:00-15:30 Automated Model Building
15:30-16:00 Validation and Deposition
16:00-16:30 Break
16:30-17:30 Introduction to CryoEM (talk)
17:30-18:00 CCP-EM (practical setup)

Tuesday, August 10

09:00-10:30 Single particle reconstruction (demo + short practical)
10:30-10:45 Coffee Break
10:45-11:15 Reconstructed volumes - interpretation, sharpening, noise reduction (practical)
11:15-12:00 De novo model building (practical)
12:00-13:00 Lunch
13:00-14:00 Model refinement and validation (practical)
14:00-15:00 Wrap-up / free time

Technical information/organizationalfor CCP4/CCP-EM

Participants will require access to a Linux or MacOS machine with CCP4 and CCP-EM installed. Access to Zoom and Slack will also be required.

CMS Workshop

Wednesday, August 11

Travel, get together dinner (paid individually)

Thursday, August 12

8:30 Arrival, coffee, instructions, meeting others  
8:50-9:00 Welcome  
9:00-9:30 Biophysics, introduction Tatsiana Charnavets
9:30-10:00 Biophysics, Advanced methods TBA
10:00-10:30 Basics of protein crystallisation Jiří Pavlíček
10:30-11:00 Crystallization of membrane proteins using lipidic systems Martin Caffrey
11:00-11:30 Coffee break  
11:30-12:00 Basics of X-ray diffraction in structural biology Jan Stránský
12:00-12:30 Protein crystallography at XFELs
Arwen Pearson
12:30-13:00 Application talk – TBA  
13:00-14:00 Lunch (local canteen)  
Practicals at instruments  
14:00-15:00 Biophysical methods Tatsiana Charnavets
15:15-15:30 short break w. coffee/tea  
15:30-16:30 Protein crystallisation Jiří Pavlíček
16:30-16:45 short break w. coffee/tea  
16:45-18:00 X-ray diffraction Jan Stránský
19:00 Dinner  

Friday, August 13

8:30-9:00 Introduction to Small angle X-ray scattering and its application in-house Jan Stránský
9:00-9:30 Advanced SAXS modeling techniques for biological macromolecules in solution Dima Molodenskyi
9:30-10:30 Mass Spectrometry Julien Marcoux + Petr Pompach
10:30-11:00 Coffee break  
11:00-12:00 Bioinformatics TBA
12:00-12:30 Application talk TBA
12:30-13:30 Lunch (local canteen)  
Practicals at instruments/computers  
13:30-14:30 Laboratory Small angle X-ray scattering Jan Stránský
14:30-14:45 short break w. coffee/tea  
14:45-15:45 Native Mass Spectrometry Petr Pompach
16:30-16:45 short break w. coffee/tea  
16:45-18:00 Bioinformatics TBA
19:00 Dinner  

All times are in CEST (UTC+2)

Confirmed speakers/tutors:

Martin Caffrey (Trinity College, Dublin); Julien Marcoux (CNRS, Toulouse); Dima Molodenskyi (EMBL, Hamburg); Arwen Pearson (Universität Hamburg); Tatsiana Charnavets (IBT); Jiří Pavlíček (IBT); Petr Pompach (IBT); Jan Stránský (IBT)