Re: [ccp4bb] What could these crystals be?

I had the same issue before. PAS should be a decent polymer for modification. On Thu, Nov 9, 2023 at 7:04 PM sadik sattar wrote: > Hi Careina, > > I hope this email finds you well. I wanted to share my experience with a > similar issue I faced in the past concerning one of my proteins, and I've

Re: [ccp4bb] What could these crystals be?

Dear Careina, I usually see such kind of "Quasi-crystal" when the folding force was not properly adjusted. Of course, you need to verify they are protein ppt before any further modifications. For these melon-seed-like crystals, the sharp-end indicated that some crystallization occurred.

Re: [ccp4bb] seek your opion on this weird diffractio pattern

> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > -- Kev

Re: [ccp4bb] Macports and Fink - failed building open source pymol on MacOS Catalina

- > > - > -- > Dr. Javier M. González > Instituto de Bionanotecnología del NOA (INBIONATEC-CONICET) > Universidad Nacional de Santiago del Estero (UNSE)

Re: [ccp4bb] how to get protein crystal

rystallization?? How to find which concentration is > enough for our target protein crystallization?? Thanks in advance > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >

Re: [ccp4bb] suggestions for cryoprotectant

; > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org/ ###

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

. I can send a script for that. > > Regards > Garib > > P.S. In spite of some unusual answers you should not be afraid asking > questions on ccp4 bb. This bulletin board is exactly for this type of > questions. > > > On 10 Sep 2018, at 18:01, Kevin Jin wrote: >

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

fense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg=A66BPdK7455wfEqkW7nlTOFIrLwyiZ0

Re: [ccp4bb] Electron density maps for Cryo-EM structures.

am particularly interested in those cryo-em structures with high >>> resolution, like 2.6~2.8A. >>> >> >> Sure, all are excited about high-res cryo-EM!!! >> >> >>> Please give me an education. >>> >> >> Sure. One of available universities c

[ccp4bb] Electron density maps for Cryo-EM structures.

Dear All, Is there any sever available to create electron density maps for cryo-em structures? Or, we should create the maps from mmCIF. I am particularly interested in those cryo-em structures with high resolution, like 2.6~2.8A. Please give me an education. Thanks, Kevin

Re: [ccp4bb] Protein Purification- reg

urify the protein. The protein PI was 6.33 > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- Kevin Jin Sharing knowledge each other

Re: [ccp4bb] Fishing crystals from volatile solvent as precipitant

Mailstop 497 > Philadelphia, PA 19102-1192 USA > > (215) 762-7706 > pjl...@gmail.com > pj...@drexel.edu > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jisc

Re: [ccp4bb] Fishing crystals from volatile solvent as precipitant

il: krey.tho...@mh-hannover.de > > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- Kevin Jin Sharing knowledge each other is always very joyful..

Re: [ccp4bb] Crystal structure of an unknown protein

-1277 or 443-3644 > > > >email : mat...@itqb.unl.pt > > > >http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography > >http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit > > > >Mailing address : > >Instituto de Tecnologia Quimica e Biologica António Xavier > >Universidade Nova de Lisboa > >Av. da República > >2780-157 Oeiras > >PORTUGAL > > > >ITQB NOVA, a great choice for your PhD > >https://youtu.be/de6j-aaTWNQ > > > >Master Programme in Biochemistry for Health > >https://youtu.be/UKstDCFjYI8 > > > -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org/

Re: [ccp4bb] Difficult purification with imac columns

inds to the resin. > Thank you in advance > Sent from my iPhone -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org/

Re: [ccp4bb] Help needed finding hit condition

> considered bubbling oxygen through and heating the sample to accelerate the > oxidation process. > > > > King Regards > > > Jonathan Bailey (PhD student) > > > Professor Martin Caffrey Lab MS group Trinity College Dublin > -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org/

Re: [ccp4bb] Protein rapidly precipitates when off ice

on buffer to rule out > concentration dependence. > > In each case, the protein precipitates to a milky solution within about a > minute of removal from ice (I am working with 20-50 uL volumes in PCR > tubes). > > Many thanks for any suggestions! > > Best, > C

Re: [ccp4bb] off topic: Alternatives to GE HiTrap columns

him. The advantage of their clone: first, high capacity and better column performance(plate numbers). On Fri, Feb 17, 2017 at 9:33 AM, Kevin Jin <kevin...@gmail.com> wrote: > Probably you can try His-Column from Clonetech (Takeda ?). They modified > the column packing using nylon mem

Re: [ccp4bb] off topic: Alternatives to GE HiTrap columns

Probably you can try His-Column from Clonetech (Takeda ?). They modified the column packing using nylon membrane, which offered better flow-through than that of traditional resin-gel column. On Wed, Feb 15, 2017 at 8:57 AM, Markus Seeliger wrote: > Dear all, > we

Re: [ccp4bb] Unknown blob extended from catalytic serine residue

> > I have tried to fit in diethylene glycol as shown in one of the attached > figures, but as observed, it is not really fit and the molecule is in > incorrect conformation. > > Kindly help me with this matter. > > > > Thanks and regards, > > Sharifah Nur Hidayah

Re: [ccp4bb] Need suggestion for protein solubility

Likely, the protein is pH sensitive. You may chain the anion and cation columns together for protein separation, then you don't need to use Imidazole. P.S. Tris pH 7.5 (RT) is ~ pH 8.2 in cold room On Sat, Dec 24, 2016 at 2:52 AM, Praveen Tripathi < tripathipraveen2...@gmail.com> wrote: >

Re: [ccp4bb] very uninformative

means something like Gold Upright Sun. Just to demonstrate how poor those things translate into reality…. ** ** PS: Orcward ligand orcs, the Amt is watching! ** ** PPS: it is still ok to ride a trolley. ** ** *From:* Kevin Jin [mailto:kevin...@gmail.com] *Sent:* Tuesday, April

Re: [ccp4bb] very informative - Trends in Data Fabrication

Dear All, Here may be another example for the importance of image storage. http://www.jinkai.org/DERA/DERA_1O0Y_3R12.html Regards, Kevin

Re: [ccp4bb] very informative - Trends in Data Fabrication

. ** ** Best, BR ** ** *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Kevin Jin *Sent:* Tuesday, April 03, 2012 3:34 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] very informative - Trends in Data Fabrication ** ** Dear All

Re: [ccp4bb] very informative - Trends in Data Fabrication

to answer. *Je pense donc je suis* Kevin On Sun, Apr 1, 2012 at 8:09 AM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: On 31/03/12 23:08, Kevin Jin wrote: I really wish PDB could have some people to review those important structures, like paper reviewer. So do the wwPDB, I would imagine

Re: [ccp4bb] very informative - Trends in Data Fabrication

Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/ -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org

Re: [ccp4bb] very informative - Trends in Data Fabrication

my data, as I did theirs ...). regards to all - Tassos (and please, no 1st April joke with fraud cases !) -- Kevin Jin Sharing knowledge each other is always very joyful.. Website: http://www.jinkai.org/

[ccp4bb] a small trick for protein and organic compound cocrystallization.

Dear All, Here is way I have used for protein and hydrophobic organic compound cocrystallization. Via this method, less amount of DMSO will be used to aviod protein ppt. I hope you can use for your research. http://www.jinkai.org/Xtal.html Regards, -- Kevin Jin Sharing knowledge each other

Re: [ccp4bb] need help for crystallization

enough. 5. Most of Phosphate buffer should be removed. That's what I used before. Let me know if it works. Best, Kevin Jin On Fri, Mar 30, 2012 at 9:40 AM, Afshan Begum afshan...@yahoo.com wrote:  Dear Kevin I have seen your website and come to you to discuss my problem actually i want

Re: [ccp4bb] dea all

kind of details or a paper that might help I will be thankful Best Regards Rana -- Kevin Jin Candle always burns itself out to light up the tunnel . Website: http://www.jinkai.org/

[ccp4bb] a small trick for SDS-Gel storage

Dear All, Maybe most of you already knew. I just put my understanding of SDS page gel storage here, if you want to make gel yourself and safe some money. http://www.jinkai.org/SDS_page.html If I am wrong, please let me know. Sharing knowledge each other is always joyful. -- Kevin Jin Protein

[ccp4bb] structure refinement and analysis work

Dear All, Do you need some help for structure refinement or structure analysis? I will be very happy to work for you, while I am looking for next position. To me, solving structure is a puzzle game and for fun. Regards, Kevin Jin

Re: [ccp4bb] My protein precipitates at r.t and dissolves at 4 oC

On Tue, Mar 13, 2012 at 8:36 AM, Min-Kyu Cho min-kyu@live.com wrote: Thank you Kevin, I will try to remove b-ME as you suggested. Min-Kyu  | -Original Message-  | From: Kevin Jin [mailto:kevin...@gmail.com]  | Sent: Monday, March 12, 2012 5:50 PM  | To: Min-Kyu Cho  | Subject

Re: [ccp4bb] My protein precipitates at r.t and dissolves at 4 oC

AM, Kevin Jin kevin...@gmail.com wrote: Hi Min, Please  try this way if you use your protein for crystallization. 1. collect the needle and run SDS page or FPLC to verify the presence of protein. Make sure it is not a buffer salt. 2. You don't need to do dialysis to remove b-ME, otherwise

Re: [ccp4bb] My protein precipitates at r.t and dissolves at 4 oC

Which kind of buffer you use? If it is Tris, then temperature change will cause pH change. Actually, this is a good way for crystallization. Kevin On Mon, Mar 12, 2012 at 9:02 AM, Min-Kyu Cho min-kyu@live.com wrote: Hi all, I have a homotetrameric coiled-coil domain sample with 45aa per

Re: [ccp4bb] My protein precipitates at r.t and dissolves at 4 oC

On Mar 12, 2012 1:11 PM, Min-Kyu Cho min-kyu@live.com wrote: I am using KPi buffer at pH 5.5, 100mM KCl, 2mM beta-mercaptoethanol, 0.02% NaN3. Yes, I agree I should check CD melting curve to see temperature preference of my protein. Min-Kyu  | -Original Message-  | From: Kevin Jin

Re: [ccp4bb] FW: endotoxin removal

To Pius, In my case, the protein/biopolymer is Lysine/amine riched. 1. Lys or Arg are mainly positively charged under pH 7.0 ~ 8.0, and then provide positively charge to LPA. Of course, some metal cations could also be involved in LPA binding. 2. Tris with the NH2 group could also be protonated

Re: [ccp4bb] FW: endotoxin removal

can test my strategy and improve it. If you can give me a feed back, there will be great! Kevin On Thu, Mar 8, 2012 at 1:01 PM, Kevin Jin kevin...@gmail.com wrote: To Pius, In my case, the protein/biopolymer is Lysine/amine riched. 1. Lys or Arg are mainly positively charged under pH 7.0

Re: [ccp4bb] FW: endotoxin removal

achieve this by buffer exchange? I wonder if an extensive wash of protein on a column would work instead. Pius On Thu, Mar 8, 2012 at 4:01 PM, Kevin Jin kevin...@gmail.com wrote: To Pius, In my case, the protein/biopolymer is Lysine/amine riched. 1. Lys or Arg are mainly positively charged

Re: [ccp4bb] FW: endotoxin removal

I tried to use 250mM Tris pH 7.6, 1M NaCl and 5~10% 2-propanol for dialysis. It works, On Wed, Mar 7, 2012 at 6:50 AM, Jerry McCully for-crystallizai...@hotmail.com wrote: Dear All;     We purified a His tag protein by Ni-NTA and gel-filtration from E.coli. We tried two

[ccp4bb] a story of Orotidine 5'-Monophosphate Decarboxylase

Dear All, I wrote a story for the catalysis of Orotidine 5'-Monophosphate Decarboxylase. http://www.jinkai.org/Enzymology.html I hope you will like it. Regards, Kevin

Re: [ccp4bb] Collecting small-molecule diffraction on a Macromolecular xtallography beam line

I collected GTP/Mg2+ crystal on SSRL beamline 9-1 before. The images was processed by Mosflm and structure was solved by Shelx as usual. Kevin On Wed, Feb 8, 2012 at 3:41 AM, Giorgio Giardina giorgio.giard...@uniroma1.it wrote: Hello, I have some interesting small molecule xtals. I was

Re: [ccp4bb] On pKa of Aspartic acid

for pKa perturbation. I am also interested in the general base of Asp and Glu in enzyme catalysis. I will be very happy to read your paper in the future. Regards, Kevin Jin On Tue, Feb 7, 2012 at 3:48 AM, Deepak Oswal deepos...@gmail.com wrote: Dear colleagues, We have solved the crystal

Re: [ccp4bb] On pKa of Aspartic acid

Maybe you would also be interested in http://www.jinkai.org/AAD_history.html Regards, Kevin On Tue, Feb 7, 2012 at 8:52 AM, Christian Roth christian.r...@bbz.uni-leipzig.de wrote: Hi, you may also look into the papers of John A. Gerlt, who did a lot on protonabtraction reactions and the

Re: [ccp4bb] On pKa of Aspartic acid

AM, Kevin Jin wrote: As we know, the pKa of water is 15.7. Under pH 7.0, its protonation should be 50/50. In this case, we may need to consider water in two formats: H2O vs. H3O+ When we say water as acid, it usually stands for H3O+ in chemistry. In chemical equation, H+ represents H3O

Re: [ccp4bb] No diffraction

For crystallization: Your xtal may come out a little bit fast. If the condition contain alcohol, such as IPA, you may have to modify it. If you let people know the condition, it may be more helpful. Also, please check the purity of your protein. Kevin On Thu, Jan 26, 2012 at 7:33 AM, Theresa

Re: [ccp4bb] No diffraction

Maybe, you can adjust the ion strength of your condition. On Thu, Jan 26, 2012 at 8:32 AM, Kevin Jin kevin...@gmail.com wrote: For crystallization: Your xtal may come out a little bit fast. If the condition contain alcohol,  such as IPA, you may have to modify it. If you let people know

[ccp4bb] A story of acetoacetate decarboxylase

Dear All, I wrote a story about the catalysis of Acetoacetate Decarboxylase. It is available here: http://www.jinkai.org/AAD_history.html http://www.jinkai.org/AAD_catalysis.html I wish you will like it. Regards, Kevin

Re: [ccp4bb] Autoreply: [ccp4bb] A story of acetoacetate decarboxylase

Dear All, I got this email. Is my account blocked? Thanks, Kevin 2012/1/24 asch...@cipf.es: Esta cuenta de correo electrónico dejara de existir dentro de 6 meses (25/05/2012). Si desea ponerse en contacto con el titular de este correo hágalo a través del siguiente e-mail:

Re: [ccp4bb] about alternate conformations

I did not make it clear. The protocol we used for protein expression always limit the occ of MSE as 0.75. You may estimate your occ of MSE by ED. You can check PDB for JCSG structures. Cheers, Kevin On Fri, Sep 16, 2011 at 7:09 AM, Ming dongm...@udel.edu wrote: Hi all, I was using Refmac

Re: [ccp4bb] QC Server (was Re: [ccp4bb] Another paper structure retracted)

? For me it keeps complaining that my sequence file is not a PIR file. The file looks OK to me, but I've never really understood what a PIR file is Phil On 12 Aug 2011, at 01:39, Kevin Jin wrote: Should we really have some crystallographers to review and qc those structures before the formal

Re: [ccp4bb] Another paper structure retracted

that my sequence file is not a PIR file. The file looks OK to me, but I've never really understood what a PIR file is Phil On 12 Aug 2011, at 01:39, Kevin Jin wrote: Should we really have some crystallographers to review and qc those structures before the formal releasing? JCSG has set