[ccp4bb] enforce planarity in user defined isopeptide link?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Weakest protein-protein complex crystallised
From: Filip Van Petegem filip {- dot -} vanpetegem {- at -} GMAIL {- dot -} COM
Date: 2008-07-01

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Subject: RE : Disordered domains in crystal strutures
From: Stephane Mouilleron Stephane {- dot -} Mouilleron {- at -} CANCER {- dot -} ORG {- dot -} UK
Date: 2008-07-01

Subject: enforce planarity in user defined isopeptide link?
From: Sarah Hymowitz hymowitz {- dot -} sarah {- at -} GENE {- dot -} COM
Date: 2008-07-01

Dear all,
I'm am trying to refine an isopeptide link in diubiquitin between a
Lys side chain and a Gly 76 C-termini. The link has reasonable
geometry (planar amide bond) prior to refinement with refmac
5.2.0019. After refinement, the peptide link is no longer planar.
Any ideas how to enforce planarity of the link?

Many thanks for any suggestions--
Sarah

refmac:
MAKE LINK Y

link statement (pdb header):
LINK NZ LYS X 48 C GLY Y
76 TRANS

CIF file for the link (generated with refmac):
global_
_lib_name mon_lib
_lib_version 4.11
_lib_update 15/04/05
#
# --- LIST OF LINKS ---
#
data_link_list
loop_
_chem_link.id
_chem_link.comp_id_1
_chem_link.mod_id_1
_chem_link.group_comp_1
_chem_link.comp_id_2
_chem_link.mod_id_2
_chem_link.group_comp_2
_chem_link.name
TRANS1 LYS . . GLY . .
bond_LYS-NZ_=_GLY-C
# ------------------------------------------------------
#
# --- DESCRIPTION OF LINKS ---
#
data_link_TRANS1
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
TRANS1 1 NZ 2 C . 1.260 0.020
# ------------------------------------------------------

------------------------------------------------------------------------
-----------
Sarah G. Hymowitz
Department of Protein Engineering
Genentech, Inc.
1 DNA Way,
South San Francisco, CA 94080

E-mail: hymowitz@gene.com
Tel: (650) 225 7819
FAX: (650) 225 3734

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Weakest protein-protein complex crystallised
From: Filip Van Petegem filip {- dot -} vanpetegem {- at -} GMAIL {- dot -} COM
Date: 2008-07-01

Next message:
Subject: RE : Disordered domains in crystal strutures
From: Stephane Mouilleron Stephane {- dot -} Mouilleron {- at -} CANCER {- dot -} ORG {- dot -} UK
Date: 2008-07-01