Hi,
We collected data using our in-house Bruker Proteum X8 diffractometer
and after using Xprep to integrate the images the output HKL file was
converted to an mtz using CCP4's Scalepack2mtz. The prp file generated
by Xprep shows good statistics with completeness and good data for 2.4
angstrom resolution. Mean intensity/sigma, Rsym, and Rsigma have good
values. Pointless indicates space group is P212121. Later we used
molecular replacement and obtained a good model and Refmac to refine the
structure. The electron density maps show the correct density for the
amino acids, waters, and other metals in the structure and refinement
with coot improves the electron density around the atoms.
However, after multiple rounds of refinement the R value drops to 0.25
but Rfree does not go below 0.35! Also, the structure factors are very
low. We have tried all the obvious reasons as not having the correct
space group which is not the case, and have included NCS restraints as
well as TLS parameters to improve the refinement. None of this has
helped in helping the Rfree value go down. Since we never have this
problem with data collected from other detectors (like at SSRL), and
this problem repeats with other datasets from collected in-house, we
suspect that the original integration of the images using Xprep might be
a problem and might be doing something to the reflection data. Does
anyone have any experience with this?
Also, I have recently tried using iMosflm to refine the data but using
the .sfrm images from the Bruker detector is problematic since I get an
Application error that reads "invalid command name" and an "Image read
error" that reads "Error reading image header. Message from Mosflm is
error reading record 33: check image is correct size". Does anyone have
any advice on how to correct this since I understand that iMosflm is
supposed to be able to read Bruker .sfrm images? Thanks! Annette
- Re: [ccp4bb] High Rfree values and using Bruker det... Annette Medina Morales
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