Hello, I would guess that the badly fitting molecule may be upside down (related my an 2-fold axis). I would use the first, partially refined structure for another round of molecular replacement in P212121 with molrep, using the model as well as a partial solution as as asearch model. The translational self peak in the native Patterson may be misleading. I came recently across a similar problem. Regards Wim
De: "Jessica Besaw" <jbesaw1...@gmail.com> À: "CCP4BB" <CCP4BB@JISCMAIL.AC.UK> Envoyé: Lundi 16 Décembre 2019 20:29:38 Objet: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density There have been two potential space groups: P212121 - Rfree = 36% P21212 - Rfree = 45% Xtriage reports that twinning is unlikely. Cheers! Jessica On Mon, 16 Dec 2019 at 13:56, Jürgen Bosch < [ mailto:jxb...@case.edu | jxb...@case.edu ] > wrote: What’s your spacegroup ? RWork / RFree? Twinning by any chance? Jürgen __________________________________________ Jürgen Bosch, Ph.D. Division of Pediatric Pulmonology and Allergy/Immunology Case Western Reserve University 2109 Adelbert Rd, BRB 835 Cleveland, OH 44106 Phone: 216.368.7565 Fax: 216.368.4223 [ https://www.linkedin.com/in/jubosch/ | https://www.linkedin.com/in/jubosch/ ] CEO & Co-Founder at InterRayBio, LLC Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology BQ_BEGIN On Dec 16, 2019, at 1:50 PM, Jessica Besaw < [ mailto:jbesaw1...@gmail.com | jbesaw1...@gmail.com ] > wrote: I am crystallizing this membrane protein in a medium (bicelles) that forms lamella like sheets that stack on top of each other. The layer packing is shown below. Is this structure unreasonable? <Screen Shot 2019-12-16 at 1.40.02 PM.png> On Mon, 16 Dec 2019 at 13:38, Reza Khayat < [ mailto:rkha...@ccny.cuny.edu | rkha...@ccny.cuny.edu ] > wrote: BQ_BEGIN Hi Jessica, The gap between the two proteins is a bit troubling. Perhaps it's the image, but why would a crystal form if there is no crystal contact between the two proteins? Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 From: CCP4 bulletin board < [ mailto:CCP4BB@JISCMAIL.AC.UK | CCP4BB@JISCMAIL.AC.UK ] > on behalf of Ashish Kumar < [ mailto:mail2ashish...@gmail.com | mail2ashish...@gmail.com ] > Sent: Monday, December 16, 2019 1:24 PM To: [ mailto:CCP4BB@JISCMAIL.AC.UK | CCP4BB@JISCMAIL.AC.UK ] Subject: [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density Hi Jessica, It may be possible because of wrong MR solution as well. How were your stats after MR. Also it is correct that it could be possible because of wrong space group. Try changing the Space group and repeat MR. Best Regards Ashish On 16 Dec 2019 22:56, "Jessica Besaw" < [ mailto:jbesaw1...@gmail.com | jbesaw1...@gmail.com ] > wrote: BQ_BEGIN Dear community, I am having a lot of trouble solving a protein structure. I think my problem may caused by incorrectly placed proteins in molecular replacement. I have two proteins in my asymmetric unit. It appears that one protein fits perfectly, and the other one has many errors. (See snapshots below). I have tried deleting the parts of the protein (and even the whole protein) to try and rebuild it in COOT, but it was a bit too difficult for me to solve. I would appreciate any and all suggestions for potential strategies moving forward. Other information: (1) 2.4 Angstrom (2) 99% complete (3) "Translational NCS may be present at a level that may complicate refinement" Cheers! Jessica <Screen Shot 2019-12-16 at 11.58.10 AM.png> <Screen Shot 2019-12-16 at 11.58.31 AM.png> To unsubscribe from the CCP4BB list, click the following link: [ https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=MBjWbF0ZDC5tg1IQYg3-zjOPSn7yuF2KfXIxak9l0MA&s=E2hs1sz4cNOm0vRwjsoHzxqEyBnMO-5BfM18hOltqLI&e= | https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ] To unsubscribe from the CCP4BB list, click the following link: [ https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=MBjWbF0ZDC5tg1IQYg3-zjOPSn7yuF2KfXIxak9l0MA&s=E2hs1sz4cNOm0vRwjsoHzxqEyBnMO-5BfM18hOltqLI&e= | https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ] To unsubscribe from the CCP4BB list, click the following link: [ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 | https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ] BQ_END To unsubscribe from the CCP4BB list, click the following link: [ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 | https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ] BQ_END BQ_END To unsubscribe from the CCP4BB list, click the following link: [ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 | https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ] ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
