[ccp4bb] ÄktaXpress to PC adapter : Off topic

[Deepak Deepak]

Dear CCP4 community,

We recently acquired some ÄktaXpress systems from our neighboring lab, but
unfortunately, we are missing the essential *adapter cable (Uninet-CAN)*.
Does your lab have this Äktaxpress cable but don't need any more,  we would
greatly appreciate your assistance.

As a point of reference, Cytiva offers this cable for approximately *3,000
USD*

1
.
Unfortunately, another company that used to provide these cables at a lower
cost now has contract agreements with Cytiva, preventing them from selling
directly to individual customers.

If you have any leads or can help us obtain the Uninet-CAN adapter cable,
that would be greatly appreciated.

Apologize for the off-topic nature of this request and sincerely appreciate
your support.

Many thanks,

Deepak



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[ccp4bb] Äktaxpress uninet connector : Off topic

[Deepak Deepak]

Dear All,

Apologies for the off-topic post.

We recently acquired some old Äktaxpress systems and learned that they
require a specific USB to Uninet cable in order to connect to a PC. For
now, we only find it on Cytiva for 2700 USD.

Could you please guide me to some other seller that might have a similar
product for cheaper or if your lab might have a spare connector?

Kind regards,
Deepak

Here is the link from cytiva
https://www.cytivalifesciences.com/en/us/shop/chromatography/tools-and-accessories/cables/akta-usb-uninet-cable-p-05948



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Re: [ccp4bb] Is the PDBe deposition server broken?

[Deepak Deepak]

Works fine on our side. Had some other issues with OneDep system yesterday,
but for now works fine.

On Fri, Oct 13, 2023 at 3:28 PM Jan Dohnalek  wrote:

> I get this when attempting to log into our current deposition session.Error:
> 500
>
> There was a technical error.
>
> Something has gone wrong with our web server when attempting to make this
> page.
>
> Unfortunately, the service you are trying to access is currently
> unavailable.
> Please try again later.
>
> --
> Jan Dohnalek, Ph.D
> Institute of Biotechnology
> Academy of Sciences of the Czech Republic
> Biocev
> Prumyslova 595
> 252 50 Vestec near Prague
> Czech Republic
>
> Tel. +420 325 873 758
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] Problem in generating restraint file for 5.2kDa ligand

[Deepak Deepak]

Dear CCP4 users,

I am working towards solving a protein-ligand complex structure. The ligand
is 5.2 kDa (495 atoms) and made of 3 distinctive repetitive monomers. I
have a PDB model for the ligand and also as smiles and mol2 format.
I tried generating restraint files for this ligand using Jligand, ProDRG,
AceDRG, Elbow (Phenix), and Gradeserver (Global phasing), but all failed to
generate the restraints. Perhaps it's too big of a molecule to handle for
restraint generation using these softwares. I checked the archived messages
on CCP4BB but could not find something helpful.

Could you advise me on how to prepare the restraints for such ligand to
proceed with the refinement?
I will happily provide more information if I am missing something here.

Kind regards,
Deepak



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[ccp4bb] suggestions on refinement of a protein-ligand complex

[Deepak Deepak]

Dear all,

Greetings from Munich. I hope everything is well with you. I am writing to
take input on a problem related to the structure solution of a
protein-ligand complex.

I have crystallized a protein (7.6kDa) with a ligand (5.2kDa). The crystal
diffracted to *2.71 Angstron*, and the data were processed using XDS.
During the XDS processing, Pointless suggested data be either P6222 (180
space group) or P6422 (181 space group) with a 98% probability.
The data were processed as *P6422*.

Afterward, I ran Phaser MR with protein's PDB as a search ensemble, and I
found a good solution (with a good TFZ score) for protein alone, where I
could see some weak density for my ligand.
In the next step, I ran Phaser MR with a *modeled PDB* of the Ligand as
search ensemble + *using the partial solution from the previous Phaser MR
run of Protein*. This Phaser MR run gave me a good fit of ligand onto
protein surface with nice density for both molecules.

Next, I went ahead with the refinement of this complex. The R-free, in the
beginning, was 0.55. In the first round of refinement, it went down to
*0.53,* but in the subsequent rounds, it even* increased*. I am stuck at
this point and unsure how to proceed. I tried different strategies to
refine it, but nothing worked.
Could the space group have been wrong? How can I make sure that? I can
provide a more detailed explanation to help you better understand the
problem.
I appreciate your suggestions and input on this matter.

Kind regards,
Deepak,
Ph.D. student,
LMU Munich, Germany.



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