Refinement Problem

Christopher W Davies

12 Jan 2011 12 Jan '11

10:12 p.m.

I am having an issue with refining my structure. I have a 2.36 A resolution dataset. I have found a solution by molecular replacement in the space group P3221. I have been refining the structure, however, my Rfactor/Rfree are not decreasing even though I have good density. My current Rfactor/Rfree values are .40/.43. Can anyone help me? Thanks. Chris

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Kelly Daughtry

12 Jan 12 Jan

10:15 p.m.

Hello Chris, The standard question here is: Are you certain of your space group? That seems to be the main culprit behind R factors that wont decrease. Can you provide some statistics showing your confidence in your space group? Kelly Daughtry ******************************************************* Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 ******************************************************* On Wed, Jan 12, 2011 at 5:12 PM, Christopher W Davies wrote:

...

I am having an issue with refining my structure. I have a 2.36 A resolution dataset. I have found a solution by molecular replacement in the space group P3221. I have been refining the structure, however, my Rfactor/Rfree are not decreasing even though I have good density. My current Rfactor/Rfree values are .40/.43. Can anyone help me?

Thanks.

Chris _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Nathaniel Echols

10:22 p.m.

On Wed, Jan 12, 2011 at 2:15 PM, Kelly Daughtry wrote:

...

The standard question here is: Are you certain of your space group? That seems to be the main culprit behind R factors that wont decrease.

Other common culprits: 1. Twinning 2. Undiagnosed translational pseudosymmetry (leading to incorrectly processed data) Xtriage will help identify space group/twinning problems. To check for (2), run labelit.index on the original images. -Nat

Christopher W Davies

10:45 p.m.

I am fairly certain that I have the correct space group. I had initially processed my data in P3, P31, and P32, however, I could not obtain a molecular replacement solution. I then went back to APS and reprocessed my data in higher space groups and I found three more space groups, P321, P3121, and P3221. P3221 was the only space group to give me a molecular replacement solution. Thanks for you help. Chris ----- Original Message ----- From: "Kelly Daughtry" To: "PHENIX user mailing list" Sent: Wednesday, January 12, 2011 5:15:40 PM Subject: Re: [phenixbb] Refinement Problem Hello Chris, The standard question here is: Are you certain of your space group? That seems to be the main culprit behind R factors that wont decrease. Can you provide some statistics showing your confidence in your space group? Kelly Daughtry ******************************************************* Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 ******************************************************* On Wed, Jan 12, 2011 at 5:12 PM, Christopher W Davies < [email protected] > wrote: I am having an issue with refining my structure. I have a 2.36 A resolution dataset. I have found a solution by molecular replacement in the space group P3221. I have been refining the structure, however, my Rfactor/Rfree are not decreasing even though I have good density. My current Rfactor/Rfree values are .40/.43. Can anyone help me? Thanks. Chris _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Pavel Afonine

13 Jan 13 Jan

12:34 a.m.

If this is the case, then just: - run AutoBuild (at 2.36A it should build your model no problems) or - try phenix.refine from the very latest PHENIX nightly build which does Dual Space Refinement (real/reciprocal) - check for twinning and if present then use it, etc... http://www.phenix-online.org/download/nightly_builds.cgi Pavel. On 1/12/11 2:45 PM, Christopher W Davies wrote:

...

I am fairly certain that I have the correct space group. I had initially processed my data in P3, P31, and P32, however, I could not obtain a molecular replacement solution. I then went back to APS and reprocessed my data in higher space groups and I found three more space groups, P321, P3121, and P3221. P3221 was the only space group to give me a molecular replacement solution.

Thanks for you help.

Chris

----- Original Message ----- From: "Kelly Daughtry" To: "PHENIX user mailing list" Sent: Wednesday, January 12, 2011 5:15:40 PM Subject: Re: [phenixbb] Refinement Problem

Hello Chris, The standard question here is: Are you certain of your space group? That seems to be the main culprit behind R factors that wont decrease. Can you provide some statistics showing your confidence in your space group?

Kelly Daughtry

******************************************************* Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 *******************************************************

On Wed, Jan 12, 2011 at 5:12 PM, Christopher W Davies< [email protected]> wrote:

I am having an issue with refining my structure. I have a 2.36 A resolution dataset. I have found a solution by molecular replacement in the space group P3221. I have been refining the structure, however, my Rfactor/Rfree are not decreasing even though I have good density. My current Rfactor/Rfree values are .40/.43. Can anyone help me?

Thanks.

Chris _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Nathaniel Echols

12:40 a.m.

On Wed, Jan 12, 2011 at 4:34 PM, Pavel Afonine wrote:

...

- run AutoBuild (at 2.36A it should build your model no problems) or - try phenix.refine from the very latest PHENIX nightly build which does Dual Space Refinement (real/reciprocal) - check for twinning and if present then use it, etc...

Just to follow up, I had a look at the Xtriage logfile, and it strongly suggests twinning (see attached image). -Nat

Pavel Afonine

12 Jan 12 Jan

10:18 p.m.

Hi Chris, hm... ok, let's start somewhere: - check for twinning: phenix.xtriage data.mtz - are you sure about space group? I guess you can ask PHASER to try all possible SGs; - run through Autobuild if get stuck, send me the data, model and sequence files and I will have a look. Pavel. On 1/12/11 2:12 PM, Christopher W Davies wrote:

...

I am having an issue with refining my structure. I have a 2.36 A resolution dataset. I have found a solution by molecular replacement in the space group P3221. I have been refining the structure, however, my Rfactor/Rfree are not decreasing even though I have good density. My current Rfactor/Rfree values are .40/.43. Can anyone help me?

Thanks.

Chris

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Christopher W Davies
Kelly Daughtry
Nathaniel Echols
Pavel Afonine