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Hi dear all:
I have three complexes of a 45 KD Fab ( two domains with a flexible hinge
region). Two of them are solved, the third has been a headache for some
complex I: space group C2; 1 mol/asyu; solvent content 59%
complex II: space group I422; 1 mol/asyu; solvent content 59%; cell
The third crystallizes in C orthorhombic, unit cell 122.7x256.7x146.8,
which processes and scales quite decently to 2.5 A. I presume similar
solvent content to I and II which leads to 4 mol/asyu. I tried finding the
MR solutions assuming both C222 and C2221 with EPMR, MOLREP and AMORE using
the complex I as a model. MOLREP is the one that seems to work better. It
appears that I have two sets of molecules related by translation. I have
two strong rotational peaks so two solutions are always quite OK but I
cannot find the other two correctly. In C222 after refinement the Rs are
above 50%; in C2221 R/Rfree is 40/47. The log file of minimization and
annealing states that parts of two NCS molecules superimpose with symmetry
mates. The maps (sa_omit and composit_omit) for C2221 look awful! I used
domain-domain NCS restraints in all refinements.
I refined and rebuilt the model with only two mol/asyu assuming C222 (
C2221 leads to R's quite above 50% after the first round of refinement).
The sa_omit_maps are great, I see perfect density for the ligand in the
active site, I almost thought I only had two molecules (80% solvent, ouch)
in the asymmetric unit but... R/Rfree got stuck at 31/33! I used this dimer
as search model (again in epmr, molrep and amore) with no better luck.
I processed and scaled and looked for molecular replacement solutions in
all other possible space groups (the details would be too lengthy but I am
sure is C orthorhombic); I collected data on crystals frozen in different
conditions and cryoprotectants and as for trying other crystallization
conditions...I've got this crystals after 150 trays, I am stuck with this
I have been thinking that my problem might be the hinge angle in the two
elusive molecules being so different from the search model that baffles the
search programs. I am a neophyte in protein crystallography so I would
appreciate any suggestions on:
1) How do I perform a search for my 4 molecules allowing for flexibility in
the hinge region?
2) If the above fails... any suggestion is more than welcome.