Hi, The density in both space groups looks very similar, with no obvious differences. The data was processed in XDS followed by refinement in REFMAC and then PHENIX.
Yes, the statistics of the orthorhombic structure is probably more realistic. But when both are refined in REFMAC these statistics are much higher (probably more at a reasonable level). I have 2 molecules in the ASU in the C2221 structure and 4 in the P21 structure. Cheers, Katherine ________________________________ From: Bosch, Juergen [[email protected]] Sent: Tuesday, July 23, 2013 2:23 PM To: Katherine Donovan Subject: Re: [ccp4bb] post to ccp4bb Hi Katherine, I would say a twin fraction of 0.5 is suspicious of a higher symmetry. In the end the density should give it away, do the side chains look as well defined in both cases ? How did you process your images Mosflm,iMosflm, HKL2000 or XDS ? As a rule of thumb you should expect R values around your resolution/10 so in the low to mid 20 - 18/23 sound reasonable for that resolution. How many molecules in the asu do you have in each case ? Jürgen On Jul 22, 2013, at 9:11 PM, Katherine Donovan wrote: Hi All, I have a data set that was collected to about 2.2A, which I have processed in either P21 (to 2.4 A) or C2221 (2.25A). I am unsure which space group is more correct. I have a higher symmetry space group with higher resolution and average statistics or a lower symmetry space group with lower resolution and great statistics. The statistics provided by aimless below. Any help would be hugely appreciated. Thanks, Katherine P21 AIMLESS P21 and cut the data to 2.4A for a Mn I/sd > 2. Average unit cell: 74.68 130 129.2 90 106.8 90 Overall InnerShell OuterShell Low resolution limit 48.09 48.09 2.44 High resolution limit 2.40 13.15 2.40 Rmerge (within I+/I-) 0.085 0.038 0.581 Rmerge (all I+ and I-) 0.099 0.042 0.687 Rmeas (within I+/I-) 0.117 0.053 0.792 Rmeas (all I+ & I-) 0.116 0.050 0.798 Rpim (within I+/I-) 0.080 0.037 0.534 Rpim (all I+ & I-) 0.059 0.026 0.405 Rmerge in top intensity bin 0.045 - - Total number of observations 352569 2057 17425 Total number unique 92184 569 4538 Mean((I)/sd(I)) 9.6 23.6 2.0 Mn(I) half-set correlation CC(1/2) 0.995 0.995 0.648 Completeness 100.0 97.2 100.0 Multiplicity 3.8 3.6 3.8 PHENIX – XTRIAGE One possible pseudo merohedral twin operator 2-fold axis h, -k, -h-l <I**2>/<I>**2 = 2.032 <F>**2/<F**2> = 0.787 <|E**2-1|> = 0.734 <|L|>, <L**2> = 0.490, 0.321 Multivariate Z score L-test = 0.616 NZ test = Maximum deviation acentric = 0.007 Maximum deviation centric = 0.051 L test = Mean L = 0.490 Estimated twin fraction: 0.450 (Britton analyses) 0.477 (H-test) 0.478 (Maximum likelihood method) Likely point group of the data is C 2 2 2 Analysis of the systematic absences indicates a number of likely space group candidates: C 2 2 21 Patterson analysis of peak with length larger than 15 Angstrom: Frac. Cood = 0.00, 0.166, 0.00 Distance to origin = 21.530 Height (origin = 100) = 3.787 p-value (height) = 9.991e-01 Final REFMAC refinement in P21 Rfactor = 0.2391 Rfree = 0.2674 After multiple rounds of refinement the twinning information is: Twin domains = 2 Twin fractions = 0.5201, 0.4799 FINAL refinement PHENIX – P21 Rwork = 0.1637 Rfree = 0.1938 Twin fraction = 0.5 for twin operator h, -k, -h-l Ramachandran outliers = 0.1% Rotamer outliers = 3.6% C-beta outliers = 0 C2221 AIMLESS Cut the data back to 2.25 for a Mn I/sd >2. Average unit cell: 74.68 247.4 130 90 90 90 Overall InnerShell OuterShell Low resolution limit 48.09 48.09 2.31 High resolution limit 2.25 9.81 2.25 Rmerge (within I+/I-) 0.117 0.044 0.984 Rmerge (all I+ and I-) 0.126 0.046 1.068 Rmeas (within I+/I-) 0.136 0.051 1.145 Rmeas (all I+ & I-) 0.135 0.050 1.147 Rpim (within I+/I-) 0.069 0.026 0.577 Rpim (all I+ & I-) 0.050 0.019 0.417 Rmerge in top intensity bin 0.050 - - Total number of observations 427886 5201 33337 Total number unique 57553 788 4433 Mean((I)/sd(I)) 11.4 32.6 2.0 Mn(I) half-set correlation CC(1/2) 0.997 0.997 0.668 Completeness 100.0 98.9 100.0 Multiplicity 7.4 6.6 7.5 First round of refinement - REFMAC – C2221 Rfactor = 0.2132 Rfree = 0.2443 Final refinement round - PHENIX – C2221 Rwork = 0.1853 Rfree = 0.2330 Ramachandran outliers = 0.1% Rotamer outliers = 7.1% C-beta outliers = 0 This email may be confidential and subject to legal privilege, it may not reflect the views of the University of Canterbury, and it is not guaranteed to be virus free. If you are not an intended recipient, please notify the sender immediately and erase all copies of the message and any attachments. Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more information. ...................... 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 This email may be confidential and subject to legal privilege, it may not reflect the views of the University of Canterbury, and it is not guaranteed to be virus free. If you are not an intended recipient, please notify the sender immediately and erase all copies of the message and any attachments. Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more information.
