SPECIAL TOPICS IN BIOCHEMISTRY: X-RAY CRYSTALLOGRAPHY-A HANDS ON WORKSHOP Syllabus

120.861.01 | AY 2013-2014 - Summer Term | 3 Credit(s)
MT 8:30:00 AM
  • Contact Information
    Faculty
    Jurgen Bosch
    Guest Faculty
    Gundula Bosch
    TA
    Lauren Boucher
  • Course Learning Objectives

    Information not required for this course type

  • Course Description

    Enables students to carry out all key steps to successfully solve and refine a protein crystal structure. Theoretical aspects are followed by application to various problem sets. Topics include tricks for data collection, data processing and refinement. Touches upon all standard techniques such as molecular replacement, SAD phasing and MAD phasing, both in theory and then applied in practical context with previously collected data. Identification of unknown ligand densities and model refinement lead to the last part of preparing publication quality figures using PyMol.

     

    Due to the blended course approach it would be useful to bring headphones with you, so you can listen to some online material while in class.

  • Intended Audience
    Ph.D students
  • Methods of Assessment

    Students are evaluated on their participation in classroom discussions and also on completion of assigned homework and tutorial data in addition to online quizzes.

  • Prerequisites
    Some basic knowledge of UNIX or Linux is desirable.
  • Course Schedule (9am - 5pm)

    Please see the course Session for a full list of dates and items for this course.

  • Academic Ethics Code

    Students enrolled in the Bloomberg School of Public Health of The Johns Hopkins University assume an obligation to conduct themselves in a manner appropriate to the University's mission as an institution of higher education. A student is obligated to refrain from acts which he or she knows, or under the circumstances has reason to know, impair the academic integrity of the University. Violations of academic integrity include, but are not limited to: cheating; plagiarism; knowingly furnishing false information to any agent of the University for inclusion in the academic record; violation of the rights and welfare of animal or human subjects in research; and misconduct as a member of either School or University committees or recognized groups or organizations.

  • Structural Biology Workshop - Letter to students

     

    Structural Biology Workshop

    Jürgen Bosch, August 2013

     

    The workshop will guide you through typical crystal structure solution scenarios. The course is designed in a very interactive way, with extensive hands-on experience. The objective is to enable you to collect X-ray diffraction data, process and evaluate datasets, and apply techniques such as molecular replacement, phasing and refinement, leading you from diffraction images to a protein structure ready for deposition in the Protein Database. You will be provided with test datasets for practicing purposes (for intellectual property reasons, you will not be allowed to bring your own data sets into the course for solution). You will learn basic methods of structural data representations for publication purposes. Course participants will form teams of two supposed to closely work together during the workshop, but each on their own computer terminal. The teams are meant to be a first go to person if you get stuck. Those teams completing their assigned tasks early, are expected to help other teams with their problem sets during the in-class sessions. Due to the blended course approach it would be useful to bring headphones with you, so you can listen to some online material while in class.

     

    “Home work” assignment prior to the workshop:

    The following programs will be used during the workshop, if you want to familiarize yourself with the interfaces that should help you during the workshop to orient yourself faster.

    MOSFLM, REFMAC, HKL2map, SNB (Shake and Bake) or BNP, Phenix, Coot, PyMOL

     

    NXClient:

    http://www.nomachine.com

    CCP4:

    http://www.ccp4.ac.uk

    Coot:

    http://www.biop.ox.ac.uk/coot/

    http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Crystallography_on_OS_X

    Phenix:

    http://www.phenix-online.org/download/

    USF packages:

    http://xray.bmc.uu.se/usf/

    PyMOL:

    http://www.pymol.org/

    OpenEye suite:

    http://www.eyesopen.com

    in particular FRED and VIDA will be used in the last session.

     

    It would be helpful to familiarize yourself with commonly used basic linux terminal commands such as cd, mkdir, pwd, ssh, scp.

     

    I am very much looking forward to seeing you all  at our workshop,

     

    Cheers,

     

    Jürgen

  • Course Format

    The course will be split in "self-paced" online tutorials and in-class hands on material. Completion of the online tutorials are required to follow the next days hands-on material.

  • Estimated Workload

    The workload may vary on your previous knowledge. However the course was re-designed to be able to allow every student to complete all assignments within the scheduled time. For those students who are extremely fast additional material will be provided for hands-on sections to challenge them with more difficult case studies.

  • Group Work Guidelines

    We will form teams of two. However each participant should work primeraly alone and when in trouble contact the teammate first. Encouraging a cummunity spirit is a desired objective of this course for your future.

  • Notes for Success

    Taking the online material serious and as a guidebook will enable you to complete the hands-on parts and assigned homeworks.

  • Disability Support Services
    If you are a student with a documented disability who requires an academic accommodation, please contact the Office of Student Life Services at 410-955-3034 or via email at dss@jhsph.edu.