WK.01 Joint Neutron and X-‐ray Structure Refinement using Joint Refine in PHENIX
This half-day workshop is intended as a somewhat informal and hands-‐on tutorial. We will have 4 organizers/hosts with extensive knowledge and experience in neutron crystallographic refinement. There has been a resurgence in macromolecular neutron diffraction over the last decade in the USA, starting with the construction of the LANL Protein Crystallography Station in ~2001. Since the early 2000s we now have another diffraction instrument, Imagine at ORNL, with a third, MaNDi at ORNL, being commissioned in 2014. This increase reflects the massive user demand for neutron diffraction instrumentation and while beam time and data collection is becoming more routine, there has been a lack of computational programs to handle the non-‐trivial refinement approach to dealing with explicit H and D atoms. The current incarnation Joint refinement in PHENIX is expected to be heavily used by a crystallographic community that is rapidly shifting to PHENIX for most refinements. Theintroductory lecture will frame the context of the workshop.This will explain the "why" of joint X-‐ray and neutron refinement for neutron studies, as well as some of the technical "how". The bulk of the workshop will focus on all the steps after neutron data collection: from preparing an appropriate PDB (is your protein hydrogenous, H/D exchangedor fully deuterated) to the finer nuances of a proper neutron/X-‐ray refinement. There will also be a focus on careful model building in Coot, taking proper hydrogen bonding and chemistry into account.
Participants will be asked to bring their own laptops with the latest version of PHENIX installed. This can be found at:
We will encourage participants that have their own neutron and isomorphous X-‐ray data sets, to bring those and work with us. We also have a high quality neutron data set of crambinto very high resolution if participants do not have their own data. This is the ideal learning data set for participants new to neutron techniques or for participants that are new to PHENIX Joint refine.
08:30 - 09:00
Set up, help participants install PHENIX, distribute practice neutron and X-‐ray data sets
09:00 - 09:30
Brief introduction on PHENIX Joint Refine, philosophy and approach, what's new and improved over previous versions
09:30 - 10:45
Participants work on PDB preparation, initial refinement parameters, making nuclear and electroni density maps for Coot, interpreting maps
10:45 - 11:00
11:00 - 12:30
Continue refinement and model building, finish structure, Q&A.
Pavel Afonine, Lawrence Berkeley National Lab
Marat Mustyakimov , Oak Ridge National Laboratory
Zoë Fisher, Los Alamos National Laboratory
Andrey Kovalevsky, Oak Ridge National Laboratory
Registration fee (regular) -‐ $100.00
Registration fee (student) -‐ $75.00