On Friday, 13 May, 2016 16:14:47 Magnus Alphey wrote:
> Dear CCP4bb,
> I am having a little issue with some data that on the surface looks OK but it is not playing ball.
> The target is a hetero-octamer - 4 each of 2 subunits.
> Autoindexing with iMosflm appears to nail the lattice as mP (Penalty of 1; next best is mC with penalty of 40)
Penalty during auto-index is one thing, success in processing is another.
Did you try integration+scaling with the mC setting?
Ethan
> Cell dimensions are 94, 147,102, 90, 102, 90.
>
> Scala gives
>
> Overall InnerShell OuterShell
> Low resolution limit 31.47 31.47 2.64
> High resolution limit 2.50 7.91 2.50
>
> Rmerge 0.120 0.039 0.710
> Rmerge in top intensity bin 0.041 - -
> Rmeas (within I+/I-) 0.144 0.047 0.859
> Rmeas (all I+ & I-) 0.144 0.047 0.859
> Rpim (within I+/I-) 0.080 0.026 0.478
> Rpim (all I+ & I-) 0.080 0.026 0.478
> Fractional partial bias -0.033 -0.012 -0.084
> Total number of observations 273802 9515 34527
> Total number unique 90106 2968 11962
> Mean((I)/sd(I)) 6.8 17.6 1.6
> Mn(I) half-set correlation CC(1/2) 0.993 0.998 0.557
> Completeness 96.8 98.3 88.6
> Multiplicity 3.0 3.2 2.9
>
> Anomalous completeness 88.5 97.2 73.5
> Anomalous multiplicity 1.6 1.7 1.6
> DelAnom correlation between half-sets -0.018 0.111 0.003
> Mid-Slope of Anom Normal Probability 0.959 - -
>
> Outlier rejection and statistics assume that there is no anomalous scattering
>
> Average unit cell: 94.03 146.71 101.90 90.00 102.41 90.00
>
> Space group: P21
>
> Average mosaicity: 0.83
>
> Minimum and maximum SD correction factors: Partials 0.65 155.76
>
>
> But then cTruncate gives
>
> TRANSLATIONAL NCS:
>
> Translational NCS has been detected at ( 0.000, 0.500, 0.500).
> The probability based on peak ratio is 0.02% that this is by chance (with resolution limited to 4.00 A).
> This will have a major impact on the twinning estimates and effectiveness of the truncate procedure
>
> Peak# Location Ratio Q-score
> 1 ( 0.00, 0.50, 0.50) 0.44 0.02
> The analysis uses the peak heights in the patterson map that are further than 14 A (approx. 4 Ca-Ca) from the origin. The presence of a large off origin peak (above 20%) and/or a very low Q-score, below 1.0, is a string indicator of the presence of tNCS. An intermidiate Q-score, between 5.0 and 1.0, may indicate weak tNCS or be the result of cross vector of a large scatterer such as a cluster or heavy metal.
>
>
> Crystals from similar drops have previously autoindexed as C2
> 101.8, 146.7, 94.9, 90, 102.5, 90
>
> Molecular replacement has not been successful (so far) and I am wondering if the translational NCS is causing an issue. Perhaps the space group/cell dimensions are not as autoindexing suggests if the tNCS interfering. Should I be treating the data some specific way ?
> If anyone has experience of this and can provide advice/suggestions, then that would be much appreciated.
>
> Kind regards,
>
> Magnus
>
>
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
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