A few things to try (or double-check):
1. If you ran phaser with SGALTERNATIVE ALL, make sure the mtz file you
gave to refmac has the same screw axes as the MR solution. If this is
off, it'll lead to higher R-factors.
2. As Fred mentioned, try with a single copy of the protein, and check
the FWT (sigma_a weighted 2Fo-Fc) maps. If the solution is reasonably
correct, you should be able to see some density for the other
components. Also, run some controls. Delete a portion of your search
model before MR, and insure that density for that region is present in
maps phased with the positioned model.
3. Use your seleniums. If your MR solution is correct, then you should
see peaks in model-phased anomalous difference maps. But confirm this
with your form_1 data. In my experience, these are not very sensitive
to model completeness (but that's with a different protein).
Since you've mentioned you're relatively new at this, you should
re-merge (scala or scalepack) as anomalous for anomalous difference maps
if you haven't done so already (normally I'd assume this was the case
for dealing with anomalous data and not mention it...sorry if I'm
telling you things you already know).
Good luck,
pm
Chao Quan wrote:
Dear CCP4 community:
I am a beginner to crystallography and therefore my apologies if this question is too
simple.
Basically we obtained several crystal forms of the same molecule, which is a
hetero-
trimer containing protein A(18kD), protein B(16kD) and a RNA segment(40nt or about
15kD).
We have solved the structure of one crystal form(form_1); its information is as
follows:
space group = P 42 22;
unit cell = 126.514 126.514 76.766 90.00 90.00 90.00
resolution = 2.7A;
Rwork = 0.25, Rfree = 0.265;
solvent content = 60%;
Number of molecules per Asymmetric Unit = 1;
Data redundancy = 5;
Data Completeness = 94%;
I am now trying to solve the structure of form_2 crystal using molecular replacement. So
far the information I know about form_2 is as follows:
space group = I 422 or I 41 22;
unit cell = 180.096 180.096 152.530 90.00 90.00 90.00
(unit cell is about 4 times the size of form_1)
resolution = 3.3A; (which is low)
Number of molecules per Asymmetric Unit = 2 or 3;
Data redundancy = 4;
Data Completeness = 92%;
There is no twinning(as shown by Sfcheck);
As shown in"Analyse Data for MR", the first peak is 100 and second is 68.92; I am not
sure if this indicates translation in a Asymmetric Unit;
The problem is, I can not get a good solution by MR using Phaser (both I422 and I4122
are tried). When I searched for 3 molecules per Asymmetric Unit, Phaser did not give
solutions at all.
When I used 2/ASU instead, I was able to get some solutions, with typical statistics as
follows:
RFZ=14, TFZ=35.9, PAK=0, LLG=1036;
However, these solutions had high R values(like Rwork=0.59 and Rfree=0.58), which
indicated that they are not solutions at all. Still, I tried refinement using refmac5, but R
values did not go down even after 50 rounds; sometimes they even increased after
refinement.
Besides, the RMS values bond length, bond angle and chiral center were all 0 as show by
refmac5.
I tried limiting resolution range to 15-4A in Phaser, which did not help either.
Now I am completely stuck. Could anyone give me some advice? I know this situation is
very strange, because I am using the SAME molecule for MR but can not can a solution.
Thanks a lot,
P.S.
1) Both form_1 and form_2 crystals were grown using Selenomethionine-containing
samples. There are 3 Sel_Met in protein A and 1 in protein B.
2) A 10-aa internal segment of protein B is missing in the solved structure, which may
indicate high flexibility.
Chao
