[ccp4bb] RES: [ccp4bb] Xray-dataset usable despite low completeness ?

Lol __ Rafael Marques da Silva Mestrando em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +55 16 99766-0021 "A sorte acompanha uma mente bem tre

[ccp4bb] RES: [ccp4bb] how to get protein crystal

group we have got better diffracting crystals using 25mg/mL) Good luck Rafael Marques da Silva Mestrando em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +55 16 99766-0021 "A sorte acompanha uma ment

[ccp4bb] [OFF TOPIC] Cell biology bb

share it with me. Kind Regards __ Rafael Marques da Silva Mestrando em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +55 16 99766-0021 "A sorte acom

[ccp4bb] RES: [ccp4bb] Looking for suggestions with protein expression

__ Rafael Marques da Silva Mestrando em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +55 16 99766-0021 "A sorte acompanha uma mente bem tre

[ccp4bb] RES: [ccp4bb] RES: [ccp4bb] Looking for suggestions with protein expression

Thank you for pointing me this out. I don’t know why I said BL21...maybe in the rush to say to use Rosetta for protein expression. We use Dh5a for plasmid replication (although I have already used BL21 for plasmid purification and it worked nicely). My bad. Rafael Marques da Silva Mestrando

[ccp4bb] CCP4 tutorials (files)

can find files for doing SAD, MAD, MR, SIRAS and so on? Many thanks in advance __ Rafael Marques da Silva Mestrando em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +55

[ccp4bb] RES: [ccp4bb] Micro/Macro crystal seeding experience

couldn’t get another space group till now. And yes, there is a lot of solvent (~79%) and I believe that this is behind with this protein crystal don’t diffract beyond the necessary. Thank you very much again, guys Best regards Rafael Marques da Silva Mestrando em Física Biomolecular

[ccp4bb] RES: [ccp4bb] Problem in real space - please sign & invite other scientists to sign this letter

eta Thunders, a sixteen years old teenager activist , is better known than the experts in the field. If we want to be believed we must take back our place. To hind is not an option. Regards Rafael Marques da Silva Mestrando em Física Biomolecular Universidade de São Paulo Bacharel em Ciên

[ccp4bb] RES: [ccp4bb] 60 kDa contamination in Rosetta cells

. Are your proteins monomers in solution? If you are not sure, try a bigger SEC column. Regards Rafael Marques da Silva Mestrando em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +55 16 99766-0021 "A

[ccp4bb] RES: [ccp4bb] 60 kDa contamination in Rosetta cells

oligomers in solution. You can try native gel to find this out but firstly I would use another SEC column, a bigger one. Superdex 200 10/300 is an analytical column and should not be used for purification itself (although I have done this many times). I would try maybe S200 16/60. Best Rafael

[ccp4bb] Postdoc position at USP (São Carlos, Brazil)

following documents for registration: – A letter presenting your interest; – A short CV, presenting academic background, publications, and information that proves your scientific experience; - Letter of recommendation. Best Regards Rafael Marques da Silva Mestrando em Física Biomolecular Universidade

[ccp4bb] RES: [ccp4bb] Coot 1

If Paul had said that there is also a Windows version I would be sure that it was April fools’ joke. I can’t wait to use it 😊 Best Rafael Marques da Silva Mestrando em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +55

[ccp4bb] RES: [ccp4bb] Off-topic question related to ITC binding studies

I am not a proper chemist, but I remember that during my college classes my professor emphasized that ^x is a measured value and not really related to stoichiometry. If someone has something to add… Best Rafael Marques da Silva Mestre em Física Biomolecular Universidade de São Paulo Bacharel

[ccp4bb] RES: [ccp4bb] Multiplicity is more than 20

Problematic is low multiplicity, not high, I’d say... Best Rafael Marques da Silva Mestre em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +55 16 99766-0021 "A sorte acompanha uma mente bem tre

[ccp4bb] Calculate charge on protein surface

would like to know “how much” red it is. Best wishes Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +55 16 99766-0021 &q

[ccp4bb] RES: [ccp4bb] Fwd: Re: [ccp4bb] Calculate charge on protein surface

will take a look on the sites and in chimera. Best wishes Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +55 16 99766-0021

[ccp4bb] RES: [ccp4bb] Is this Spam? This looks like Spam.

The same happened to me. I had to subscribe again cause I was not receiving ccp4 mails anymore. Best Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal

[ccp4bb] Updated pbd metrics and other small things

scattering, could you please send me? I am preparing a presentation and a single google search has been really misleading. Best wishes Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de São Paulo Bacharel em Ciências

[ccp4bb] [OFF TOPIC] On Ni-NTA resin TEV cleavage

resin (or maybe do not add both). I saw that someone did not have EDTA and used b-mercap. instead of DTT. May I have your comments if you guys already faced a similar situation? Best wishes __ Rafael Marques da Silva PhD Student – Structural

[ccp4bb] RES: [ccp4bb] About model building

Hi Sam. If you still have any of your crystals or any protein solution left in the well you harvested your crystals, I would run a MS/MS with them. Next step would be to run AF with your known chain A and your best Mass Spec hit (s), and use the resulting model for MR. Good luck Rafael

[ccp4bb] RES: [ccp4bb] What could these crystals be?

diffract, I think it is something you should try with the remaining ones. Alternatively, if you have a source of UV light coupled to a camera, they should “light up”. I wish you the best of luck. Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física

[ccp4bb] RES: [ccp4bb] low resolution data refinement

it using an in-house system you should consider a synchrotron light source. Best wishes Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos

[ccp4bb] RES: [ccp4bb] What could these crystals be?

Hi all. Just wanted to add a bit of doubt to the topic. Is it possible that they are salt crystals? I don’t know, but some spots are too intense and far from each other to me. But maybe I just need better glasses. Best wishes Rafael Marques da Silva PhD Student – Structural Biology University

[ccp4bb] RES: [ccp4bb] Crystals with DNA

concentration? Best wishes Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +55 16 99766-0021 "A sorte acompanha uma ment

[ccp4bb] RES: [ccp4bb] Rwork and Rfree the same?

3.2 A structure. How such a nice map could have been calculated with such poor parameters? I could only think of anisotropy. Best Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de São Paulo Bacharel em Ciênc

Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

I tried it yesterday and I was really shocked by how fast it is. When I was preparing to submit my second job, the first one was already finished, which made me think that I was definitely doing something wrong. Probably I was...Best wishes Rafael Marques On 13 May 2024 09:53, Harry Powell

[ccp4bb] RES: [ccp4bb] What could these crystals be?

It seems to me that your drop has dried. By the pic, I would not say these are crystals Best Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São

[ccp4bb] RES: [ccp4bb] Crystal optimization

Hi, It seems to my eyes that you have multiple nucleation events happening simultaneously. I would recommend you to try crystallization under 10 or 4 ºC Best of luck Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de

[ccp4bb] RES: [ccp4bb] message yesterday on the CCP4BB

It reminds me of that movie, the wishmaster, a thrash one. “Be careful about what you desire” Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São

Re: [ccp4bb] Unknown density

Dear John Ethanol would be my first guess, Best wishes __ Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestrando em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas

Re: [ccp4bb] how to create a figure of a blob

I would suggest the same Best __ Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestrando em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São

[ccp4bb] [OFF-TOPIC] Dissolving DMPC/ Na Cholate in buffer for nanodisc assembly

what I am getting. I wonder if someone experienced this issue before and could shed light in how it was solved. Best wishes __ Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestrando em Física Biomolecular

Re: [ccp4bb] [OFF-TOPIC] Dissolving DMPC/ Na Cholate in buffer for nanodisc assembly

Hi all, yes, it was a typo. I have twice the amount of Na cholate than DMPC, in this case 200 mM. Best wishes PS: I will answer individually to all of you. Thanks in advance for your help. __ Rafael Marques da Silva PhD Student

Re: [ccp4bb] Recommendations for crystallization screens

Hi Saniya, In general I don't have a preferred kit to try. I try all the ones that are available. More you try, more chances you have. Best wishes ______ Rafael Marques da Silva PhD Student – Structural Biology University of Leic

Re: [ccp4bb] Crystal optimization

? These crystals look ideal for it. I would also reccommend leaving your plates at cold temperature (10 or 4ºC). This will slow down your nucleation events increasing the likelihood of bigger crystals. Best wishes Rafael Marques da Silva PhD

Re: [ccp4bb] Modelling unidentified ligand

I am probably wrong, but to me it looks like PEG. Maybe a small peptide product of degradation? Best wishes __ Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de

Re: [ccp4bb] enzyme or other protein with multiple cofactors

Hi Harry I always think about big regulatory complexes when it comes to this. 2G28, a pyruvate dehydrogenase, or 8FWP, a septin that regulates the cell cycle in yeast, might answer the question you are looking for. Best wishes __ Rafael

Re: [ccp4bb] unknown density

Hi Michael, It looks like PEG to me too. Have you used a smaller PEG as cryoprotectant. Such as PEG 200 or PEG400? Also, as an off topic thing, why are you refining hydrogens at this resolution? Best wishes __ Rafael Marques da Silva PhD

Re: [ccp4bb] unknown density

__ Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de São Carlos phone: +44 07861 273773 "A sorte acompanha uma ment

Re: [ccp4bb] [OFF-Topic] GST-tagged protein refold protocol

ne could really 'see' whether molecules...were just as experiments suggested?" – Dorothy Hodgkin From: CCP4 bulletin board on behalf of Rafael Marques Sent: 11 March 2025 11:18 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] [OFF-Topic] GST-tagged protein refold protocol    

[ccp4bb] Move a loop in a modelling software

not want to do. Any suggestion? Best wishes ______ Rafael Marques da Silva PhD Student – Structural Biology University of Leicester Mestre em Física Biomolecular Universidade de São Paulo Bacharel em Ciências Biológicas Universidade Federal de Sã

Re: [ccp4bb] Crystallization of SARS-CoV-2 3CLpro and Mutants – Seeking Advice on Crystal Optimization

Hi Mohit, I would also recommend mixing your fresh seeds with fresh protein and redoing the crystallization screenings. Sometimes a different cryoprotectant may enhance your resolution. Best wishes __ Rafael Marques da Silva PhD Student