Re: [ccp4bb]: refmac5 geometry restraints

[Garib N Murshudov <garib@ysbl.york.ac.uk>]

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SD - CE distance is correct and sigma is large. It is from Engh and Huber as 
far as I remember. I have seen strange behaviour of Mets and usually they are 
due to multiple conformations of side chain of Met. Usually comparison of B 
values of CE , SD and CG show that. Electron density may also show pecular 
deinisty of indication. And there is always choice to create your own MET 
dictionary wiht CE-SD sigma smaller. I would check electron density and 
B-values first.

regard
Garib

On Thursday 18 Jul 2002 6:00 pm, Wolfram Tempel wrote:
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>
> Dear colleagues:
> this is about some trouble I am having with methionine bond lengths.
> This problem is NOT shown on PROCEHECK's geometrical distortion summary
> page but comes up in PDB/ADIT's "validation" summary letter.
>
> Deviation  Residue  Chain  Sequence  AT1  -  AT2    Bond    Dictionary
>               Name     ID     Number                 Distance    Value
> ------------------------------------------------------------------------
>    -0.358     MET        A    101      SD   -  CE     1.433     1.791
>    -0.228     MET        B    101      SD   -  CE     1.563     1.791
>    -0.218     MET        B    132      SD   -  CE     1.573     1.791
>
> When manually corrected (geometry refinement in Xtalview) refmac
> restores the shorter bond distances. My diagonal weighting term is at
> 0.25 for 1.8 A data and appears to be a reasonable choice: no other
> significant distortions are found and geometry RMSD are ok.
> I looked at $CBIN/data/monomers/mon_lib_prot.cif:
>
> loop_
> _chem_comp_bond.comp_id
> _chem_comp_bond.atom_id_1
> _chem_comp_bond.atom_id_2
> _chem_comp_bond.type
> _chem_comp_bond.value_dist
> _chem_comp_bond.value_dist_esd
>   MET        N    H       coval       0.860    0.020
>   MET        N    CA      coval       1.458    0.019
>   MET        CA   HA      coval       0.980    0.020
>   MET        CA   CB      coval       1.530    0.020
>   MET        CB   HB1     coval       0.970    0.020
>   MET        CB   HB2     coval       0.970    0.020
>   MET        CB   CG      coval       1.520    0.030
>   MET        CG   HG1     coval       0.970    0.020
>   MET        CG   HG2     coval       0.970    0.020
>   MET        CG   SD      coval       1.803    0.034
>   MET        SD   CE      coval       1.791    0.059
>   MET        CE   HE1     coval       0.960    0.020
>   MET        CE   HE2     coval       0.960    0.020
>   MET        CE   HE3     coval       0.960    0.020
>   MET        CA   C       coval       1.525    0.021
>   MET        C    O       coval       1.231    0.020
>
> and changed both CG-SD and SD-CE esd's to 0.02 with no effect.
> I am using refmac5 as distributed with CCP4-4.2.1 (intel linux).
> How can I selectively enforce stronger restraints for selected bonds in
> selected residues?
> I am grateful for any suggestions.
> Wolfram Tempel
> U. of Georgia

-- 
Garib N. Murshudov, Chemistr Department, University of York
Tel: (01904) 432565