Re: [ccp4bb] To Trim or Not to To Trim

[mesters@biochem]

Dear all,

to trim or not to to trim….

- what is the difference between highly disordered side-chain atoms versus 
disordered bulk-solvent atoms? Do not both represent a continuum function with 
a comparable electron-density distribution? Have not solvent and side-chain 
atoms merged/mixed at this position in space and with this, are effectively 
indistinguishable (contrast loss i.e. similar contribution to diffraction) from 
one another?

- are current solvent models comprehensive enough in that modelling of atoms 
with very high B factors is really mutually beneficial for bulk and structure 
model?

- is model bias (overfitting) not increased by modelling highly disordered 
side-chain atoms (Rfree will probably not increase but R will drop)?

- analogous to the disordered side-chain atoms, bulk solvent atoms are of 
course also present in the crystal, so why not fill the AU with solvent 
molecules and let refinement take care of them?
(published methodology, see https://doi.org/10.1107/S0907444906021627 
)


Trimming or non-evidence-based placement and refinement are somehow halfhearted 
options with split opinions among the community as the discussions demonstrate.

Adding/Modelling a plausible side-chain rotamer with zero occupancy still has 
its charm and better reflects the situation "the side-chain atoms must be there 
but we do not know exactly where"……..

Cheers

Jeroen





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Re: [ccp4bb] Rational mutations and crystallizability

[mesters@biochem]

Sorry/Correction, the link I send is apparently also obsolete: The page is 
still accessible but no jobs can be submitted.

Workaround might be, use XtalPred-RF and use the information/outcome for 
guidance to mutate your protein sequence of interest…...

Best 

J.
--
Dr. math. et dis. nat. Jeroen R. Mesters
https://orcid.org/-0001-8532-6699


University of Lübeck
Institute of Biochemistry
https://www.biochem.uni-luebeck.de
phone: +49-451-3101-3105
Ratzeburger Allee 160
23562 Lübeck
Germany
--

> Am 08.03.2023 um 13:42 schrieb mesters@biochem 
> :
> 
> 
> https://services.mbi.ucla.edu/SER/intro.php 
> <https://services.mbi.ucla.edu/SER/intro.php>
> 
> Best
> 
> J.
> 
> 
> --
> Dr. math. et dis. nat. Jeroen R. Mesters
> https://orcid.org/-0001-8532-6699 <https://orcid.org/-0001-8532-6699>
> 
> University of Lübeck
> Institute of Biochemistry
> https://www.biochem.uni-luebeck.de <https://www.biochem.uni-luebeck.de/>
> phone: +49-451-3101-3105
> Ratzeburger Allee 160
> 23562 Lübeck
> Germany
> --
> 
>> Am 08.03.2023 um 12:05 schrieb  > <mailto:vito.calder...@unifi.it>>:
>> 
>> Dear All,
>>  
>> I remember that 10-15 years ago there was at least one website 
>> predicting/suggesting residue mutations potentially able increase 
>> crystallizability of a protein.
>>  
>> I recall, for example, http://www.doe-mbi.ucla.edu/Services/SER 
>> <http://www.doe-mbi.ucla.edu/Services/SER> but it is not working any longer.
>>  
>> Some of the sites I found nowadays predict the ‘chances’ to crystallize a 
>> protein but they do not seem to propose any possible mutation.
>>  
>> Is anyone aware of any server that provides info on specific mutations which 
>> might lead to better crystallizability?
>>  
>> Best regards
>>  
>> Vito Calderone
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
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>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>




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Re: [ccp4bb] Rational mutations and crystallizability

[mesters@biochem]

https://services.mbi.ucla.edu/SER/intro.php 


Best

J.


--
Dr. math. et dis. nat. Jeroen R. Mesters
https://orcid.org/-0001-8532-6699

University of Lübeck
Institute of Biochemistry
https://www.biochem.uni-luebeck.de
phone: +49-451-3101-3105
Ratzeburger Allee 160
23562 Lübeck
Germany
--

> Am 08.03.2023 um 12:05 schrieb  :
> 
> Dear All,
>  
> I remember that 10-15 years ago there was at least one website 
> predicting/suggesting residue mutations potentially able increase 
> crystallizability of a protein.
>  
> I recall, for example, http://www.doe-mbi.ucla.edu/Services/SER 
>  but it is not working any longer.
>  
> Some of the sites I found nowadays predict the ‘chances’ to crystallize a 
> protein but they do not seem to propose any possible mutation.
>  
> Is anyone aware of any server that provides info on specific mutations which 
> might lead to better crystallizability?
>  
> Best regards
>  
> Vito Calderone
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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Re: [ccp4bb] NMR structires

[mesters@biochem]

Maybe intensional to stress the word „paradoxal“ included in the title of the 
deposition? Same could be true for the related entry 1HIS to stress the word 
„dynamics“?

I guess back in in 1993-1994, structures were not checked rigorously…

Jeroen
--
Dr. math. et dis. nat. Jeroen R. Mesters
https://orcid.org/-0001-8532-6699
University of Lübeck
Institute of Biochemistry
https://www.biochem.uni-luebeck.de
phone: +49-451-3101-3105
Ratzeburger Allee 160
23562 Lübeck
Germany
--

> Am 02.03.2023 um 16:09 schrieb Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>:
> 
> I have been looking at 1hiq - an NMR structure with 20 models.
> I had always assumed that an attempt had been made to overlap the first with 
> the second, third etc, but this does not seem to be so for this structure..
> Have I been labouring under a misapprehension?
> Eleanor Dodson
> 
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Re: [ccp4bb] complementarity between the protein and the ligand/compound

[mesters@biochem]

Could this be what you are looking for? 
http://biosig.unimelb.edu.au/csm_lig/prediction 


J.
--
Dr. math. et dis. nat. Jeroen R. Mesters
https://orcid.org/-0001-8532-6699
University of Lübeck
Germany
--
> Am 12.02.2023 um 03:34 schrieb Xin Huang 
> <0317accc4341-dmarc-requ...@jiscmail.ac.uk>:
> 
> Dear All,
> 
> Does anyone know a server for calculation/analysis of the complementarity 
> between the protein and the ligand/compound from a co-crystal structure (of 
> the protein with the ligand/compound)?
> 
> Thanks.
> 
> 
> Best regards,
> Xin
> 
> 
> 
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Re: [ccp4bb] 3d stereo on windows 10/11

[mesters@biochem]

Active stereo support is slowly dying and the hardware will fail in the end 
(sorry to say)…. 

One possible alternative is a passive stereo PluraView 
 , which is expensive 
 but compatible with software such as YASARA, 
ChimeraX, PyMOL, Maestro, SYBYL-X, etc.

Regards

J.

> Am 10.02.2023 um 16:34 schrieb Krishnan Raman :
> 
> What is the best current hardware setup for 3d stereo on windows OS.
> Nividia does not support 3d vision anymore.
> Iam still hanging onto to the old system with p5000 Quadro cards. Would like 
> to know what  other alternatives are available?
> Regards
> Krish
>  
> 
> 
> 
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Re: [ccp4bb] Ice Lamellar formation over the MicroTube - Oxford cryo stream 700

[mesters@biochem]

Hi,

As far as the nitrogen stream delivery system is concerned
- remove the leg(s) from the empty dewar and let it warm up to room temperature
- make sure the dewar has not collected ice at the bottom. If it has, remove 
the ice and let the dewar dry
- connect a high-vacuum turbo-pump to the leg valve, start the pump and once 
the pump runs quietly, open the valve and let the pump run for many hours while 
warming-up the lower end of the leg (hot-air gun but do not turn the heat on 
full power, warm is sufficient). Close valve and turn off the pump
- place the leg(s) back into the dewar and fill it up

As for the AD51 unit
- maintenance is due every 15000 hours (yours shows 26000 hours)
- for sure you need to replace the carbon impregnated seals on the oil-free 
compressor pump heads* (not rocket science)
- replace the compressor delivery filter too
- check that all air and purge valves are working

*Quote from the maintenance manual, page 6: The eventual failure of the cup 
seal is a very sudden process and the dryness of the dry air will deteriorate 
rapidly, also the maximum flowrate of dry air will drop below 25 litres/minute 
(perhaps less than 10 litres/minute).


Good luck,

J.
--
Dr. math. et dis. nat. Jeroen R. Mesters
https://orcid.org/-0001-8532-6699



University of Lübeck
Institute of Biochemistry
https://www.biochem.uni-luebeck.de
phone: +49-451-3101-3105
Ratzeburger Allee 160
23562 Lübeck
Germany
--

> Am 09.02.2023 um 09:14 schrieb Natesh Ramanathan :
> 
> After they saw via video call that the Dry Air Unit was not maintaining more 
> than 15 L/min Air flow, even after adjusting the flow rate knob..  they gave 
> a  quote for service...As always, the cost of the service engineer visit 
> and spares were prohibitively expensive and... 




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Re: [ccp4bb] Regarding the diffraction image

[mesters@biochem]

A and B unit cell dimensions are hardly bigger than twice the uni cell of cubic 
NaCl and will probably not accommodate a 30 kDa protein.

Make a SDS gel of washed & dissolved crystals to be sure these are not alt or 
inhibitor crystals. You can stain the crystals with IzIt...

J.

--
Dr. math. et dis. nat. Jeroen R. Mesters
https://orcid.org/-0001-8532-6699



University of Lübeck
Institute of Biochemistry
https://www.biochem.uni-luebeck.de
phone: +49-451-3101-3105
Ratzeburger Allee 160
23562 Lübeck
Germany
--

> Am 03.02.2023 um 09:22 schrieb kavyashreem :
> 
> Dear all,
> 
> We crystallized a protein (30kDa) + ligand (by cocrystallization), in the 
> condition 10%PEG3350, 50mM Zinc acetate.
> Protein was in the buffer 20mM HEPES, 150mM NaCl, 1uM ZnCl2, 4mM TCEP, pH 8. 
> Crystal: Crystal:   
> crystal under UV m
> <8ef9453e.png>
> When we collected the data at an in-house facility, it looked something like 
> this:
> 
> The minimum resolution spot is around 9Ang and maximum ~2.2Ang. 
> I have not come across a protein diffraction like this, nor of a salt. When I 
> ran the gel for the incubated protein (protein+ligand), there was no 
> degradation.
> Although, I was sure there is some problem with this image I tried 
> processing, which could not be, But indexing showed a unit cell  of 11Ang, 
> 11Ang, 46Ang in P3. which was quite expected for two of the axes but not the 
> third.
> Can anyone please shed some light on this diffraction image?
> How can it happen?
>  
> Thank you
> Regards
> Kavya
>  
> 
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