[phenixbb] Non-standard residue numbers in NCS restraints

Sampson, Jared Jared.Sampson at nyumc.org
Thu Dec 23 08:11:56 PST 2010

Greetings all,

My lab is working on a 3.2Å resolution structure with 6 NCS copies of an antibody Fab fragment with insertions in its CDR loops.  The residue numbers of CDR loop H3, for example, include 100A, 100B, etc. in each of the heavy chains (Kabat numbering).  There are observable differences between NCS copies in parts of the model due to crystal contacts and so forth, so we want to exclude those residues from the NCS. Phenix.refine, when given NCS restraints like the example below, produces a result with much higher R/Rfree values than when the same structure was run with "normal" continuous numbering (R/Rfree of .26/.30 compared to .21/.26 before changing to Kabat numbering).

Reference selection:
chain H and (resseq 1:100A or resseq 100H:113)
Restrained selection:
chain I and (resseq 1:100A or resseq 100H:113)

Phenix version is 1.6.4-486.

Any thoughts on what might be causing this or how to account for the non-standard numbers in NCS restraints?


Jared Sampson

Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
New York, NY 10016

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