Hi Pramod,
1. You should try to identify the correct space group first. Did you
integrate in p1 and run pointless?
2. A template with 31% identity is not a great model. The number of
molecules in ASU will affect your chances of success. Hopefully it's not
large. wrfac of 0.6 and Rfree of 0.5 suggest the solution may be
incorrect. Did you try phaser?
3. Did you check for twinning?
Thanks,
Abhinav
JCSG@SSRL, SLAC
(650) 926-2992
On 06/17/2013 09:35 AM, Pramod Kumar wrote:
Dear group
I have a crystal data diffracted around 2.9 A*,
during the data reduction HKL2000 not convincingly showed the space
group (indexed in lower symmetry p1), while the mosflm given
C-centered Orthorhombic, and again with little play around HKL2000
given CO, now the model for molecular replacement with closest
identity of 31 given a contrast of 2, score 0.30 and wrfac 0.60. but
"balbes" uses different models with lesser identity,
no matter which way I am going the rFree keep on increasing during
refinement in refmac, when I build the model in coot with deletion and
addition of residue it starts with relatively low but gradually rises
through almost all cycles although model fits to the density well and
residue are building, coot validation parameters are also reasonable
OK for geometry, rotamer, density fit,..
now my question....
* where should i first check for possible correction?
* In molecular replacement what should be the red line for identity
and related criteria?
* if initial rFree starts around 50, how likely that its not the right
way?
* my rms bond angle is close to 1 while the bond length is 0.01 and
chiral 0.1 concludes what is serious?
*sincere apology for amateur query* if any...
thanks in advance
pramod
--
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Pramod Kumar.
Graduate Student.
Crystallography lab.
Department Of Biotechnology.
Indian Institute Of Technology Roorkee
Uttranchal.247667
India
+919359189657.
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