Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density
Dear Jessica, Good to hear that you've solved it! We're currently putting a lot of work into making the tNCS treatment in Phaser more robust. Would it be possible to share more information about your case so we can understand why it was necessary to manually turn off tNCS in that case? Having the data (which we would only use for this purpose) would be best, if you could send that off-line. If you don't feel able to share the data, then sample log files from an unsuccessful run and the eventual successful run might give us some hints. Best wishes, Randy Read > On 16 Dec 2019, at 21:29, Jessica Besaw wrote: > > THE PROBLEM IS SOLVED! > > Thank you all for you suggestions. I applied all the suggestion across all > datasets collected (not just the one shown above). > > The error & solution: Incorrect space group assignment (new space group P 21 > 2 21) and ignoring tNCS. > > This is the BEST Christmas gift a crystallographer could get. Thank you > everyone! > > Cheers! > > Jessica > > > > > > > > > > > > > On Mon, 16 Dec 2019 at 16:16, Wim Burmeister <mailto:wim.burmeis...@ibs.fr>> wrote: > 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" mailto:jbesaw1...@gmail.com>> > À: "CCP4BB" mailto: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>> 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 > > On Dec 16, 2019, at 1:50 PM, Jessica Besaw <mailto: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? > > > > On Mon, 16 Dec 2019 at 13:38, Reza Khayat <mailto:rkha...@ccny.cuny.edu>> wrote: > 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>> on behalf of Ashish Kumar > mailto:mail2ashish...@gmail.com>> > Sent: Monday, December 16, 2019 1:24 PM > To: CCP4BB@JISCMAIL.AC.UK <mailto: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>> wrote: > 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 wh
Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density
THE PROBLEM IS SOLVED! Thank you all for you suggestions. I applied all the suggestion across all datasets collected (not just the one shown above). The error & solution: Incorrect space group assignment (new space group P 21 2 21) and ignoring tNCS. This is the BEST Christmas gift a crystallographer could get. Thank you everyone! Cheers! Jessica On Mon, 16 Dec 2019 at 16:16, Wim Burmeister wrote: > 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" > *À: *"CCP4BB" > *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 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/ >> >> CEO & Co-Founder at InterRayBio, LLC >> >> Johns Hopkins University >> Bloomberg School of Public Health >> Department of Biochemistry & Molecular Biology >> >> On Dec 16, 2019, at 1:50 PM, Jessica Besaw 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? >> >> >> >> On Mon, 16 Dec 2019 at 13:38, Reza Khayat wrote: >> >>> 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 on behalf of Ashish >>> Kumar >>> *Sent:* Monday, December 16, 2019 1:24 PM >>> *To:* 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" wrote: >>> >>> 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 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>>
Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density
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" À: "CCP4BB" 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? 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 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=DwMFaQ=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0=MBjWbF0ZDC5tg1IQYg3-zjOPSn7yuF2KfXIxak9l0MA=E2hs1sz4cNOm0vRwjsoHzxqEyBnMO-5BfM18hOltqLI= | https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=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=DwMFaQ=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0=MBjWbF0ZDC5tg1IQYg3-zjOPSn7yuF2KfXIxak9l0MA=E2hs1sz4cNOm0vRwjsoHzxqEyBnMO-5BfM18hOltqLI= | https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 ] To unsubscribe from the CCP4BB list, click the following link: [ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 | https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 ] BQ_END To unsubscribe from the CCP4BB list, click the following link: [ https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 | https://www.jiscmail.ac.uk/cgi-bin/we
Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density
Hi Jessica You may try the following (if you haven't already): 1. Try solving it using P222 space group. 2. Re-index using different axes. *Regards* *Adarsh Kumar* *Florida State University College of Medicine* *Tallahassee, FL - 32304* On Mon, Dec 16, 2019 at 2:30 PM Jessica Besaw wrote: > 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 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/ >> >> CEO & Co-Founder at InterRayBio, LLC >> >> Johns Hopkins University >> Bloomberg School of Public Health >> Department of Biochemistry & Molecular Biology >> >> On Dec 16, 2019, at 1:50 PM, Jessica Besaw 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? >> >> >> >> On Mon, 16 Dec 2019 at 13:38, Reza Khayat wrote: >> >>> 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 on behalf of Ashish >>> Kumar >>> *Sent:* Monday, December 16, 2019 1:24 PM >>> *To:* 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" wrote: >>> >>> 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 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> -- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0=MBjWbF0ZDC5tg1IQYg3-zjOPSn7yuF2KfXIxak9l0MA=E2hs1sz4cNOm0vRwjsoHzxqEyBnMO-5BfM18hOltqLI=> >>> >>> >>> >>> -- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0=MBjWbF0ZDC5tg1IQYg3-zjOPSn7yuF2KfXIxak9l0MA=E2hs1sz4cNOm0vRwjsoHzxqEyBnMO-5BfM18hOltqLI=> >>> >>> -- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >>> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> >> >> > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
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 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/ > > CEO & Co-Founder at InterRayBio, LLC > > Johns Hopkins University > Bloomberg School of Public Health > Department of Biochemistry & Molecular Biology > > On Dec 16, 2019, at 1:50 PM, Jessica Besaw 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? > > > > On Mon, 16 Dec 2019 at 13:38, Reza Khayat wrote: > >> 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 on behalf of Ashish >> Kumar >> *Sent:* Monday, December 16, 2019 1:24 PM >> *To:* 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" wrote: >> >> 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 >> >> >> >> >> >> >> >> >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0=MBjWbF0ZDC5tg1IQYg3-zjOPSn7yuF2KfXIxak9l0MA=E2hs1sz4cNOm0vRwjsoHzxqEyBnMO-5BfM18hOltqLI=> >> >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0=MBjWbF0ZDC5tg1IQYg3-zjOPSn7yuF2KfXIxak9l0MA=E2hs1sz4cNOm0vRwjsoHzxqEyBnMO-5BfM18hOltqLI=> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] 1 out of 2 proteins in asymmetric unit does not fit density
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/ CEO & Co-Founder at InterRayBio, LLC Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology > On Dec 16, 2019, at 1:50 PM, Jessica Besaw 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? > > > > On Mon, 16 Dec 2019 at 13:38, Reza Khayat <mailto:rkha...@ccny.cuny.edu>> wrote: > 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>> on behalf of Ashish Kumar > mailto:mail2ashish...@gmail.com>> > Sent: Monday, December 16, 2019 1:24 PM > To: CCP4BB@JISCMAIL.AC.UK <mailto: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>> wrote: > 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 > > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0=MBjWbF0ZDC5tg1IQYg3-zjOPSn7yuF2KfXIxak9l0MA=E2hs1sz4cNOm0vRwjsoHzxqEyBnMO-5BfM18hOltqLI=> > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0=MBjWbF0ZDC5tg1IQYg3-zjOPSn7yuF2KfXIxak9l0MA=E2hs1sz4cNOm0vRwjsoHzxqEyBnMO-5BfM18hOltqLI=> > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
