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[ccp4bb]: Data processing
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Dear CCP4ers,
I have a non-CCP4 problem:
dataset at 3 A resolution, synchrotron source, 1 degree frames, 180
degrees; frozen crystal, reasonable mosaicity.
Denzo table looks like this:
------------------------------------------------------------------------
Lattice Metric tensor Best cell (symmetrized)
distortion index Best cell (without symmetry restrains)
primitive cubic 14.85% 88.62 151.10 89.21 90.00 86.54 89.81
109.64 109.64 109.64 90.00 90.00 90.00
I centred cubic 26.41% 121.89 174.91 175.47 43.38 110.35 110.11
157.42 157.42 157.42 90.00 90.00 90.00
F centred cubic 26.61% 198.76 193.90 194.36 77.78 53.58 54.03
195.68 195.68 195.68 90.00 90.00 90.00
primitive rhombohedral 14.09% 174.91 151.10 175.47 30.56 40.71 30.44
167.16 167.16 167.16 33.90 33.90 33.90
105.25 105.25 471.14 90.00 90.00 120.00
primitive hexagonal 12.17% 88.62 89.21 151.10 90.00 90.19 93.46
88.91 88.91 151.10 90.00 90.00 120.00
primitive tetragonal 1.44% 88.62 89.21 151.10 90.00 90.19 93.46
88.91 88.91 151.10 90.00 90.00 90.00
I centred tetragonal 9.71% 88.62 89.21 325.58 75.07 75.38 93.46
88.91 88.91 325.58 90.00 90.00 90.00
primitive orthorhombic 1.43% 88.62 89.21 151.10 90.00 90.19 93.46
88.62 89.21 151.10 90.00 90.00 90.00
C centred orthorhombic 0.18% 121.89 129.49 151.10 89.87 90.14 89.62
121.89 129.49 151.10 90.00 90.00 90.00
I centred orthorhombic 9.71% 88.62 89.21 325.58 75.07 75.38 93.46
88.62 89.21 325.58 90.00 90.00 90.00
F centred orthorhombic 9.45% 121.89 129.49 325.58 89.73 68.15 89.62
121.89 129.49 325.58 90.00 90.00 90.00
primitive monoclinic 0.08% 88.62 151.10 89.21 90.00 93.46 89.81
88.62 151.10 89.21 90.00 93.46 90.00
C centred monoclinic 0.17% 121.89 129.49 151.10 89.87 90.14 89.62
121.89 129.49 151.10 90.00 90.14 90.00
primitive triclinic 0.00% 88.62 89.21 151.10 90.00 89.81 86.54
autoindex unit cell 88.62 89.21 151.10 90.00 89.81 86.54
------------------------------------------------------------------------
Indexing in primitive tetragonal or orthorhombic fails. C centred
orthorhombic, monoclinic, and triclinic all work nicely, and indexing and
integration are apparently OK.
The problems start when scaling the data: all possibilities, except for
triclinic, produce unreasonable results (using 'default parameters').
Ridiculously high chi squares (50 or more!) in the first round, Rmerges
over 50%, huge rejection files (half the data!). In the following rounds,
chi squares 'drop' to 2 or so, but the rejection files grow even bigger,
and Rmerges are stuck.
Well, it must be triclinic...but the refined cell is the following:
89.211 89.214 150.819 90.000 89.989 87.153 ----> a=b, alpha=beta=90.
Furthermore, assuming a 50% water content, I would have 10 molecules in the
cell; a bit unlikely, and a real molecular replacement nightmare. On the
other hand, the low resolution diffraction limit could hint at loose
packing and high water content, and things might not be that bad.
Any ideas or suggestions? Where should one look for possible problems or
mistakes (before scaling)? I must confess my unease with symmetry, maybe
the Denzo table is showing me something that I cannot see.
Thanks to everybody,
Carlo
------------------------------------------------
Carlo Ciatto Tel. 0041 1 6356563
Biochemistry Institute University of Zuerich
190 Winterthurerstrasse 8057 Zurich Switzerland
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