# No subject

Mon Mar 12 09:43:37 PDT 2012

```The full list of Patterson peaks is:

=A0 x =A0 =A0 =A0y =A0 =A0 =A0z =A0 =A0 =A0 =A0 =A0 =A0height =A0 p-value(h=
eight)
( 0.500, 0.500, 0.165 ) : =A0 78.635 =A0 (6.634e-07)
( 0.000, 0.000, 0.330 ) : =A0 56.292 =A0 (2.795e-05)
( 0.500, 0.500, 0.497 ) : =A0 30.920 =A0 (1.207e-03)
( 0.500, 0.500, 0.187 ) : =A0 =A04.873 =A0 (9.347e-01)

=A0If the observed pseudo translationals are crystallographic
=A0the following spacegroups and unit cells are possible:

=A0space group =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0operator =A0 =A0 =A0 =A0 unit=
cell of reference setting
=A0 =A0 I 4 2 2 (a,b,3*c) =A0 x+1/2, y+1/2, z+1/6 =A0(191.70, 191.70, 103.6=
8,
90.00, 90.00, 90.00)

Secondly, for your I4 datasets, if the resoluiton of your
I422_xtriage.log file is correct (2.76 angstroms), then an=A0=A0r=3D29% and
r-free=3D34% is not too far off, using the general rule of thumb that a
structure=A0is close to completion when the r-factors are 10 times the
resolution. For example, resolution of 2.7 a r-factor around 27%
should indicate that the structure is close to finished.
Ultimately, it's your manual inspection and judgement (aside from
statistics) that dictate=A0whether=A0you think the structure to be fully
refined.

Hope that helps,
Kelly

*******************************************************
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 Mon, May 7, 2012 at 10:50 AM, Zhou, Tongqing (NIH/VRC) [E]
<tzhou at mail.nih.gov> wrote:
>
> Dear All,
>
>
>
> I have collected several dataset for an antibody:antigen complex. It appa=
rently 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=A0 (18 cha=
ins total ). However, ridigbody and subsequent refinement with TLS could no=
t reduce the r and r-free which stayed at ~48%. Tried to go P4, P222=85(12 =
mol/ASU) with twinning, but the refinement failed due to insufficient compu=
ter 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 redu=
ced to 1/3 of that of P4. With the I4 data (~2.7 A resolution), I422 was th=
e best MR space group (1 mol/ASU), the refinement went down to r=3D29% and =
r-free=3D34%, but won=92t go down further.
>
>
>
>
>
>
>
>
> Tongqing
>
>
>
> 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)
>
> *************************************************************************=
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```