[phenixbb] Difficult dataset and refinement--P422? I422?Twinning?

Zhou, Tongqing (NIH/VRC) [E] tzhou at mail.nih.gov
Mon May 7 07:50:54 PDT 2012

Dear All,

I have collected several dataset for an antibody:antigen complex. It apparently indexed to P4 space group with large cell dimensions of 191.7000/191.7000/311.0540. When I processed as P1 and ran Pointless, it suggested P422 as space group. P4212 gives the best MR solution with 6 mol/ASU  (18 chains total ). However, ridigbody and subsequent refinement with TLS could not reduce the r and r-free which stayed at ~48%. Tried to go P4, P222...(12 mol/ASU) with twinning, but the refinement failed due to insufficient computer memory (12 GB), it was also impossible to refine in P1 due to the same reason.

But for some data sets, HKL2000 also gave I4 space group with c axis reduced to 1/3 of that of P4. With the I4 data (~2.7 A resolution), I422 was the best MR space group (1 mol/ASU), the refinement went down to r=29% and r-free=34%, but won't go down further.

Please advise if it's possible to use the data


Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4609B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120507/e22b86e9/attachment-0001.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: p422_xtriage.log
Type: application/octet-stream
Size: 47126 bytes
Desc: p422_xtriage.log
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120507/e22b86e9/attachment-0002.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: I422_xtriage.log
Type: application/octet-stream
Size: 19753 bytes
Desc: I422_xtriage.log
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120507/e22b86e9/attachment-0003.obj>

More information about the phenixbb mailing list