[phenixbb] Using experimental phases in refinement

Kumar, Abhinav abhinavk at slac.stanford.edu
Sat Oct 26 09:41:35 PDT 2013

We at JCSG follow the following protocol for all structure solution/refinement:
1. Experimental phasing: location of heavy atoms either by shelx or solve.
2. If shelx is used for heavy atom location, refine those coordinates with sharp and phase.
3. The resultant solve.mtz or eden-unique.mtz file contains HL coefficients. Use these HL coefficients in refinement.

In your case, you can directly feed the heavy atom positions from your model to solve or sharp.

Abhinav Kumar, Ph.D.
Joint Center for Structural Genomics
SSRL, SLAC National Accelerator Laboratory
2575 Sand Hill Rd, Menlo Park, CA 94025
(650) 926-2992

On Oct 26, 2013, at 8:42 AM, Joseph Noel <noel at salk.edu<mailto:noel at salk.edu>> wrote:

Hi Folks,

I am wondering if anyone can recommend some good reference(s) of structure refinements that employed experimental phases. We are attempting to collect experimental phases for a series of structures for which we have refined the structure already. I assume we can easily use initial model phases (space group doesn't change) to locate anomalous scatters and calculate experimental phases from the elucidation of the heavy atom arrangement.

Most of the structures range from 1.7 to 2.4 A resolution. Would also appreciate any advice on the most efficient and accurate set of steps to accomplish this. If anyone thinks that this will not add much to the refinement of these structures would also appreciate some critiques.

The protein in question crystallizes with 68% solvent content and one monomer per assymetric unit. We are employing ensemble refinement as the protein in question displays local conformational changes depending on the type of ligand(s) bound and also pH and similar but distinct crystallization conditions. We are carrying this out on ~400 mutants to do a very large scale comparison.

Sorry for the long email but since we want to try and understand even minor conformational changes I thought phased-refinement would be much more powerful then refining just against the Fs.

Thanks again in advance,

Joseph P. Noel, Ph.D.
Arthur and Julie Woodrow Chair
Investigator, Howard Hughes Medical Institute
Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
The Salk Institute for Biological Studies
10010 North Torrey Pines Road
La Jolla, CA  92037 USA

Phone: (858) 453-4100 extension 1442
Cell: (858) 349-4700
Fax: (858) 597-0855
E-mail: noel at salk.edu<mailto:noel at salk.edu>

Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ

Homepage Salk: http://www.salk.edu/faculty/noel.html
Homepage HHMI: http://hhmi.org/research/investigators/noel.html

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