[ccp4bb] electrostatic potential and charged residues
Hi all, I'm working on a protein structure which showed a special electrostatic potential on its surface: positive on one end and negative on the other end. I wonder to what extent I can say this pattern is determined by the charged residues? If the residues are conserved, could I make a conclusion that its homologues also have such pattern? Thanks! The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[ccp4bb] correlations of B-factors and resolution
Dear all, I have a 2.4A structure(pdb code 3LAF)with an average protein b-factor of 48. I wonder whether it's acceptable. Is there a direct correlation of b-factor and resolution? The R and Rfree are 21.1% and 23.1%, respectively. This structure has a very high solvent content, 75%. Does it affect the b-factors? Thanks a lot! Qiang The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [ccp4bb] correlations of B-factors and resolution
Hi, Thanks for all the suggestions and comments! I have 1635 reflections(5.0%)for the test set. PDB_REDO gives lower R and Rfree. Shall I refine it further and re-deposit it? Thanks! Hi Tim, With small test sets, R-free doesn't become meaningless you just have to take into account that R-free has an error margin which is higher than for cases with a large test set. Few people report this error margin, but with a small data set you can easily do K-fold cross validation. I.e. do K refinements with K = 1/(test set fraction) and report R and R-free as averages with a standard deviation (instead of what we call cross validation, but is actually holdout validation). The CCP4 program freerflag already splits your data set in K groups to make it easier for the user. I do this automatically in PDB_REDO if the test set contains fewer than 500 reflections. It's amazing how much R-free is influenced by the choice of ones test set. Cheers, Robbie Date: Wed, 16 May 2012 16:06:24 +0200 From: t...@shelx.uni-ac.gwdg.de Subject: Re: [ccp4bb] correlations of B-factors and resolution To: CCP4BB@JISCMAIL.AC.UK -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Qiang, without much explanation, rather from experience, the average B-factor rises as resolution drops. It does make sense in a way because high B-factors indicate some degree of disorder and disorder is usually the cause for the resolution limit. 48A^2 for a 2.4A structure sound perfectly fine with me, I would not worry provided that all other statistices seem sound. High solvent content surely affects the B-values. The larger the solvent channels and smaller the contact area between the molecules, the more likely they become less stable and less ordered. R and Rfree seem also very good, although the gap is relatively tight. Did you make sure your Rfree set contains at least 500 reflections? The default of 5% often used, can lead to fewer reflections than 500 at medium or low resolution, and with less than 500 reflection Rfree becomes statistically meaningless - at least according to Axel Brunger's article about that topic. Cheers, Tim On 05/16/12 15:46, Qiang Chen wrote: Dear all, I have a 2.4A structure(pdb code 3LAF)with an average protein b-factor of 48. I wonder whether it's acceptable. Is there a direct correlation of b-factor and resolution? The R and Rfree are 21.1% and 23.1%, respectively. This structure has a very high solvent content, 75%. Does it affect the b-factors? Thanks a lot! Qiang The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPs7RgUxlJ7aRr7hoRAnS8AJ472kwIWxf7rqDOhEPSBG5ipvQOWQCeNHNk bum4yGTB56Wtt0JbkixleCw= =uIfE -END PGP SIGNATURE-
[ccp4bb] Positions in Structural Biology of Signaling and HIV-related Immunology
There are two immediate openings for protein crystallographer position in Harvard Medical School. One of the research projects is focused on the structural and functional investigation of Wnt signaling pathway. The project is the close collaborative efforts between Professor Xi Hes lab at Childrens Hospital and Jia-huai Wangs lab at Dana-Farber Cancer Institute. The other project is to study protective role of cellular immunity against HIV, which is a collaboration between Professors Bruce Walkers lab at Ragon Institute and Jia-huai Wangs lab. The successful candidate should have a Ph.D. in structural biology. The candidate will be responsible for determining crystal structure using X-ray crystallography. He/she should also have experience in molecular biology and protein biochemistry, capable in cloning and protein expression and purification. Interested candidates can email a CV, three contacts for reference, as well as an email address and a telephone number to Dr. Jia-huai Wang at jw...@red.dfci.harvard.edu. For more information regarding the Wang Laboratorie, please see the website: http://wang.dfci.harvard.edu The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[ccp4bb] Position in Structural Biology of Signaling
There is an immediate opening for a protein crystallographer position in Harvard Medical Schools Childrens Hospital. The research is focused on the structural and functional investigation of Wnt signaling pathway. The project is the close collaborative efforts between Professors Xi He and Jia-huai Wangs labs. The successful candidate should have a Ph.D. in structural biology. The candidate will be responsible for determining crystal structure using X-ray crystallography. He/she should also have experience in molecular biology and protein biochemistry. Interested candidates can email a CV, three contacts for reference, as well as an email address and a telephone number to Dr. Jia-huai Wang at jw...@red.dfci.harvard.edu or Dr. Xi He at xi...@childrens.harvard.edu. For more information regarding the Wang and He Laboratories, please see the website: http://wang.dfci.harvard.edu and http://www.childrenshospital.org/cfapps/research/data_admin/Site160/mainpageS160P0.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [ccp4bb] real dimer vs crystal packing
Thanks, Artem! PDE2A also uses three domains to form a homodimmer. However, without the catalytic domain, the GAF B domain swings out. This is an excellent example for the restrictions set by the multidomain context. Anyone knows other examples? Thanks a lot! PDE2 full length versus domain only structures, I think. Artem On Thu, Jan 12, 2012 at 10:03 AM, Qiang Chen c...@red.dfci.harvard.eduwrote: Hi, I'm working on a multi-domain protein which uses three domains to form homodimer, and the full-length structure is available. We have solved the structure of one binding domain alone and found its homo-binding mode is totally different from that of the full-length protein. Do you know examples or papers discussing the similar subjects (crystal packing shows false binding mode)? Thanks a lot! Qiang The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[ccp4bb] real dimer vs crystal packing
Hi, I'm working on a multi-domain protein which uses three domains to form homodimer, and the full-length structure is available. We have solved the structure of one binding domain alone and found its homo-binding mode is totally different from that of the full-length protein. Do you know examples or papers discussing the similar subjects (crystal packing shows false binding mode)? Thanks a lot! Qiang The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[ccp4bb] multi domain restriction for protein binding
Hi guys, I'm working on a multi-domain protein which uses three domains to form homodimer, and the full-length structure is available. We have solved the structure of one binding domain alone and found its homo-binding mode is totally different from that within the context of the full-length protein. I think the other domains may set some restrictions for the binding mode of the one we've solved. Do you know examples or papers discussing the similar subjects? Thanks a lot! Qiang The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[ccp4bb] Postdoctoral fellow position in structural biology
Peking University, College of Life Sciences seeks to recruit dedicated postdoctoral fellows to carry out structural and functional investigation of cell surface receptors in nervous systems. The successful candidates will focus his/her research on elucidation of molecular mechanism with which these receptors play the part in neuronal development and the immune function in central nervous system (CNS). These include their functions in axon guidance, synapse formation and neuron-glia interaction that mediates key immunological protection for CNS. The project is the close collaborative efforts between Professor Jia-huai Wang's structural biology lab and Professor Yan Zhang's neuroscience lab. Position requires PhD. degree with a good background in molecular biology, protein chemistry and crystallography. Highly motivated individuals are encouraged to apply. The position will be based at Peking University in Beijing, China, with opportunity of doing some research at Harvard Medical School in Boston. Peking University is one of the leading academic institutions in China. The College of Life Sciences is equipped with the state-of-art facilities in structural biology for X-ray crystallography, NMR, EM and single molecule studies. The well-known beautiful campus is located at Chinas most advanced academic center with more than 100 research institutes and a dozen highly respected universities. Historically Peking University also has a large international community and attracts students and postdoctoral fellows from all over the world. Interested candidates please email a cover letter, CV, 3 reference names, as well as email address and telephone number to Drs. Jia-huai Wang or Yan Zhang at jw...@red.dfci.harvard.edu and yanzh...@pku.edu.cn. For more information on Wangs group, please see the website: http://wang.dfci.harvard.edu The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[ccp4bb] O-linked glycosylation refinement in Phenix
Dear all,
I'm refining a structure which has both N-linked and O-linked
glycosylation. I use Phenix to do the refinement. It works well for the
N-linked NAG. I defined the link as the following:
apply_cif_link {
data_link = NAG-ASN
residue_selection_1 = chain A and resname NAG and resid 701
residue_selection_2 = chain A and resname ASN and resid 518
}
But it doesn't work when I defined the fucose-threonine link as the
similar way:
apply_cif_link {
data_link = FUC-THR
residue_selection_1 = chain A and resname FUC and resid 801
residue_selection_2 = chain A and resname THR and resid 596
}
The error message is missing CIF link: data_link_FUC-THR.
Does anyone have the experience of the O-linked glycosylaton refinement by
Phenix?
Thanks a lot!
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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[ccp4bb] Postdoctoral fellow position in structural biology
Dear all, on behalf of Jia-huai Wang, I post this message. For inquiries please contact Jia-huai at jw...@dfci.harvard.edu. Postdoctoral fellow position in structural biology Peking University, College of Life Sciences seeks to recruit dedicated postdoctoral fellows to carry out structural and functional investigation of cell surface receptors in immune and nervous systems. The successful candidates will focus his/her research on elucidation of molecular mechanism with which these receptors play the part in neuronal development and the immune function in central nervous system (CNS). These include their functions in synapse formation and neuron-glia interaction that mediates key immunological protection for CNS. The project is the close collaborative efforts between Professor Jia-huai Wang's structural biology lab and Professor Yan Zhang's neuroscience lab. Position requires PhD. degree with a strong background in molecular biology and protein chemistry. Experiences in crystallography and/or neuroscience will be a plus, but not absolutely required. Highly motivated individuals are encouraged to apply. The position will be based at Peking University in Beijing, China, with opportunity of doing some research at Harvard Medical School in Boston. Peking University is one of the leading academic institutions in China. The College of Life Sciences is equipped with the state-of-art facilities in structural biology for X-ray crystallography, NMR, EM and single molecule studies. The well-known beautiful campus is located at Chinas most advanced academic center with more than 100 research institutes and a dozen highly respected universities. Historically Peking University also has a large international community and attracts students and postdoctoral fellows from all over the world. Interested candidates please email a cover letter, CV, 3 reference names, as well as email address and telephone number to Drs. Jia-huai Wang or Yan Zhang at jw...@red.dfci.harvard.edu and yanzh...@pku.edu.cn. For more information on Wangs group, please see the website: http://wang.dfci.harvard.edu The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[ccp4bb] twinned?
Hi all, The data I am working on has a strong translation vector. The space group is C2221 and resolution is 2.3 angstrom. There are two molecules per AU with a pseudo-2-fold axis. On the cumulative intensity distribution plot, the theor and obser curves totally do not overlap. I did detect_twinning from CNS, and there is the result: |I|^2/(|I|)^2 = 3.2236 (2.0 for untwinned, 1.5 for twinned) (|F|)^2/|F|^2 = 0.6937 (0.785 for untwinned, 0.865 for twinned) Does the result mean my data is not twinned? Any suggestion will be highly appreciated. Thank you! The information transmitted in this electronic communication is intended only for the person or entity to whom it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this information in error, please contact the Compliance HelpLine at 800-856-1983 and properly dispose of this information.
