> Hope this helps,
> Tristan
>
> On 18 Jun 2021, at 05:05, Prem Prakash wrote:
>
> Dear all,
> Sorry for this off topic. I am working on an enzyme that has an
> exonuclease activity. The enzyme preferentially cleaves an unprocessed
> substrate at a faster rate than th
Hi Saif,
If your goal is to perform co-crystallization, I am completely agreed with
David's suggestions. Delta Tm does matter in the co-crystallization but
that's not always the case. I have some experience with protein complexes
where I successfully co-crystallized by using really high molar rat
Hi Lumbini,
There are couple of queries I have before commenting on this issue.
1) how many Cysteine residues are there in your protein
2) have you calculated their solvent accessible surface area ?
3) What is the final concentration of Sodium dithionite ?
Cysteine is highly prone to get thiol
>> >
>>
>>
>> ---
>> Patrick J. Loll, Ph. D.
>> Professor of Biochemistry & Molecular Biology
>> Drexel University College of Medicine
>> Room 10-
there
any thumbrule for this ratio, and how it is dependent on the resolution of
the data. Please shed some light on these aspects.
Thank you
With kind regards
Prem
--
With kind regards,
Prem Prakash
PhD Research Scholar
Protein Crystallography Lab
Biosciences and Bioengineering
IIT Bombay
t;CCP4BB@JISCMAIL.AC.UK"
> *Subject: *[ccp4bb] protein quasicrystals?
>
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks like
> multiple lattices. I
Is that positive density lying at the symmetry axis ? please check, if yes
then probably you have to model the appropriate compound with appropriate
occupancy.
Best
Prem
On Fri, Jan 26, 2018 at 11:10 PM, Vivoli, Mirella
wrote:
> Hi Tristan!
> Definitely PEG, in the so called horseshoe shape.
-- Forwarded message --
From: Prem Prakash
Date: Fri, Dec 29, 2017 at 10:22 AM
Subject: Re: [ccp4bb] how to improve the diffraction quality of the
crystals and avoid icerings
To: zaigham mahmood khan
Hi, Yuvraj
Initially I also faced similar problems, then I tried various
What is your occupancy of PEG here ?,you should also look at it.
Best
Prem
On Thu, Dec 14, 2017 at 6:37 AM, sanjeev kumar
wrote:
> Thanks, I'll check it out.
>
> On Wed, Dec 13, 2017 at 8:06 PM Anthony Addlagatta <
> anthonyaddlaga...@gmail.com> wrote:
>
>> This could be 2-mercaptoethanol.
>>
>
I generally add Protease inhibitor cocktail in cell lysate (calbiochem set
II) which have almost all required protease inhibitors, and each time I got
the crystal, without any effect due to this. You should be also careful if
your protein itself is a protease as many times people find these
inhibit
Hi Mubinur,
I got the same situation while refining my protein complex with Lanthanum
ion complex, reducing the occupancy while refining solved the problem.
Good luck
P.P
On Thu, Jun 15, 2017 at 11:17 PM, Pavel Afonine wrote:
> Hi Mubinur,
>
> try without "metal restraints" and see if that helps
Dear Rohit,
I am totally agree with Mark, that just R free and R work does not decide
the structure solved, you have to see other parameters as Mark already
suggested. What is and redundancy and also what is the mosaicity? please
look at these parameters too.
Best
Prem
On Wed, Dec 14, 2016 at 10:
Hello Wei,
There is a simple way of assessing the Biphenyl in your condition is as
follows:
1) You can take you concentrated mother liquor (given: if you are sure no
aromatic compound is available in ML) and take a absorption spectra at
wavelength range of 200-300, if you get a maxima at near about
It seems your chain ID is different, so it would not connect two different
chain ID covalently. So please change your chain ID and try to connect.
Good luck
On Sat, May 23, 2015 at 3:53 PM, Ishan Rathore
wrote:
> Dear All,
>
> I am sorry to disturb you all with this silly question, but this pr
Hi,
It happened with me also, thought I had not the needles but the crystals.
Temperature matters a lot in these situations, leave the trays unattended
for long and also try with various concentration. Make it highest say 15
mg/ml and dilute serially to set with a range of concentrations. Sometime
With due respect ! I want to ask that,
If it is protonated at neutral pH, what about the local pka of the active
site key residues involved ? would not it make any difference if it adds
extra H-atom and actual case is different when the reaction is carried out
?
With Kind regards
Prem
On Fri, A
Best wishes,
>
> Randy Read
>
> On 2 Dec 2013, at 04:11, Prem Prakash wrote:
>
> > Dear All,
> >
> > The density obtained after molecular replacement using phaser at 2.5
> Angstrom and then used buccneer for autobuilding of the model. I am not
> getting reaso
Dear All,
The density obtained after molecular replacement using phaser at 2.5
Angstrom and then used buccneer for autobuilding of the model. I am not
getting reasonable R value (it is 38.5 %) but the figure of merit is 0.629.
As My protein has two domains. So is it possible to fragment the indiv
I have processed my Data with XDS, here the completeness is 95.5% after
merging two data sets of the same crystals (initially it was 90% when was
not merged) at the scaling step and R-factor is 18.5 and I/sigma is 1.45.
and I further went with this data for molecular replacement where the
Z-value
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