Hi Jason, don't really think that the overall scaling stats look very good. Even for such a long unit cell, we have plenty of in-house data (even with a smaller detector) with much lower Rmerge, typically below 0.15. Possibly monoclinic with beta close to 90deg? This might also explain the shifting distance you mention. Check the detailed output of the pointless log file, not only the last few lines. Check the section where Rmeas is reported for each symmetry element. If you have one or two axes sticking out a bit there, reduce symmetry. This table of pointless has shown to be most valuable in several cases.
Good luck. Cheers, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com On Jul 16, 2012, at 8:28 PM, Jason Busby wrote: > Hi, > > The autoindexing picks this unit cell pretty much unambiguously, and the > profiles look reasonable. These are crystals of a very large heterodimer > (2177 residues), and this unit cell would have 2 heterodimers and 56% > solvent, which seems reasonable. Scaling and merging produce reasonable > statistics (I used aimless, not XSCALE): > Overall InnerShell OuterShell > Low resolution limit 19.91 19.91 3.04 > High resolution limit 2.99 16.38 2.99 > > Rmerge (within I+/I-) 0.339 0.040 0.907 > Rmerge (all I+ and I-) 0.348 0.045 0.949 > Rmeas (within I+/I-) 0.360 0.042 0.994 > Rmeas (all I+ & I-) 0.359 0.046 0.997 > Rpim (within I+/I-) 0.119 0.014 0.393 > Rpim (all I+ & I-) 0.085 0.012 0.291 > Rmerge in top intensity bin 0.053 - - > Total number of observations 1981569 5075 44784 > Total number unique 112524 338 4559 > Mean((I)/sd(I)) 10.6 53.4 2.6 > Mn(I) half-set correlation CC(1/2) 0.993 0.999 0.527 > Completeness 98.8 43.7 82.1 > Multiplicity 17.6 15.0 9.8 > > > Rmerge is high in the outer shell, but looks ok to me across the rest of the > data. The oscillation angle is correct. > > The native data set also indexes with the same spacegroup and a slightly > smaller unit cell (a=134 b=148 c=274), I attributed the difference to the Pt > soak. > > The only ambiguity is one of the screw axes, so it may be P22121 or P212121. > My XDS.INP has SPOT_RANGE commented out so I believe the default is to use > all the data for indexing. > > Cheers, > > Jason. > -- > Jason Busby > PhD Student > Laboratory of Structural Biology > School of Biological Sciences > University of Auckland > Thomas Building 110 > 3a Symonds St > Private Bag 92019 > Auckland 1142 > New Zealand > > ph: +64 9 3737599 ext 84155 > fx: +64 9 3737414 > > On 17/07/2012, at 3:02 PM, Bosch, Juergen wrote: > >> Hi Jason, >> >> if you look at the generated profiles in INTEGRATE.LP do they seem >> reasonable ? >> Does XSCALE.LP produce reasonable I/SigI statistics and expected Rvalues ? >> If not this might be another hint at wrong cell/spacegroup perhaps. >> You can try collecting spots from your whole data set with SPOT_RANGE= >> [start frame] [end frame] and then index the data. If you get too many >> strong spots you can select the top 5000 from SPOT.XDS. >> Is the oscillation correct in your script ? >> >> Jürgen >> >> P.S. we just collected some data on a 460Å cell >> >> On Jul 16, 2012, at 5:52 PM, Jason Busby wrote: >> >>> Hi, >>> >>> I have a crystal with a large unit cell in P21221 (a=134 b=151 c=276) and >>> I'm wondering if I have a problem with overlaps. I have a native dataset, >>> and am trying to get phases. I've collected a Pt soak data set on our home >>> source with a 0.5˚ oscillation angle, but the anomalous signal drops off >>> after about 8Å. I am wondering if this is a problem due to overlaps at >>> higher resolution. >>> >>> The Pt dataset has been integrated with XDS, and there don't seem to be too >>> many rejects, but looking at FRAME.CBF it looks like the predicted spots >>> are overlapping at higher resolution. You can see a zoomed-in part of >>> FRAME.CBF here: >>> http://imgur.com/1WShV >>> >>> Should I be concerned with this? The crystal mosaicity from XDS is 0.25, >>> so fairly low. What can I do about this, should I try smaller oscillation >>> angles? >>> >>> Thanks, >>> >>> Jason. >>> >>> -- >>> Jason Busby >>> PhD Student >>> Laboratory of Structural Biology >>> School of Biological Sciences >>> University of Auckland >>> Thomas Building 110 >>> 3a Symonds St >>> Private Bag 92019 >>> Auckland 1142 >>> New Zealand >>> >>> ph: +64 9 3737599 ext 84155 >>> fx: +64 9 3737414 >>> >> >> ...................... >> Jürgen Bosch >> Johns Hopkins University >> Bloomberg School of Public Health >> Department of Biochemistry & Molecular Biology >> Johns Hopkins Malaria Research Institute >> 615 North Wolfe Street, W8708 >> Baltimore, MD 21205 >> Office: +1-410-614-4742 >> Lab: +1-410-614-4894 >> Fax: +1-410-955-2926 >> http://lupo.jhsph.edu >> >> >> >> >
