[ccp4bb] I222 - P22121 space-group ambiguity
Hi everybody, I collected a number of X-ray data sets from crystals originating from the same cryst. drop. I solved the initial structure in P22121 space group by MR with Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree: 0.213/0.244. Processing of some of the other data sets with XDS/Aimless is consistent with I222 space group (resolution ~ 2.6 Ang.). I can locate one molecule. The unit-cell dimensions for I222 and the initial P22121 space groups for two of the data sets are: I222: a=87.8 b=101.18 c=123.63; P22121: a=93.34 b=105.47 c=122.98; I superposed the molecule in I222 onto one of the two located for the initially solved P22121; the orientation of the NCS-related molecule in P22121 differs from the crystallographic-symmetry related one in I222. Trying to solve this P22121 data set in I222 with MR, does not result in high Z scores, and maps do not look good. Some of the data sets that process in I222 to ~ 3 Angstr., I can also solve in P22121, locating two molecules (differences may not be that clear in this case, since the resolution is lower). Some other data sets process in P22121 with Aimless; with a substantial off-origin Patterson peak, indicating translational NCS. For these, Phaser positions two molecules that are related by crystallographic translational NCS. These two molecules are crystallographic-symmetry related in the original P22121 data set. I can also solve these data sets in I222 space group, with the overall Z score higher than for the P22121 data. I am uncertain, what the ‘true’ space group for some of my data sets is. Could it be that for data that process in P22121, but can be solved in I222, reflections that would indicate I222 space group were not collected? Alternatively, perhaps what I am seeing is that there is a (gradual) transition of the crystal lattice (between P22121 and I222 or vice versa), caused by variation in crystal handling/cooling or exposure to X-rays. It’s relevant to me, because in P22121 space group, a region of the molecule that is of biological interest makes NCS-related crystal contacts that are crystallographic-symmetry related in I222. Has anybody observed similar cases? I would appreciate comments. Cheers, Florian
Re: [ccp4bb] I222 - P22121 space-group ambiguity
Hmmm - well the I212121 cell and the P21221 cells you give here have different volumes, so they cant be just rearrangements of symmetry operators and non-cryst translation. Do you get other sets of cell dimensions for different processing? Eleanor On 13 October 2014 09:47, Florian Schmitzberger schmitzber...@crystal.harvard.edu wrote: Hi everybody, I collected a number of X-ray data sets from crystals originating from the same cryst. drop. I solved the initial structure in P22121 space group by MR with Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree: 0.213/0.244. Processing of some of the other data sets with XDS/Aimless is consistent with I222 space group (resolution ~ 2.6 Ang.). I can locate one molecule. The unit-cell dimensions for I222 and the initial P22121 space groups for two of the data sets are: I222: a=87.8 b=101.18 c=123.63; P22121: a=93.34 b=105.47 c=122.98; I superposed the molecule in I222 onto one of the two located for the initially solved P22121; the orientation of the NCS-related molecule in P22121 differs from the crystallographic-symmetry related one in I222. Trying to solve this P22121 data set in I222 with MR, does not result in high Z scores, and maps do not look good. Some of the data sets that process in I222 to ~ 3 Angstr., I can also solve in P22121, locating two molecules (differences may not be that clear in this case, since the resolution is lower). Some other data sets process in P22121 with Aimless; with a substantial off-origin Patterson peak, indicating translational NCS. For these, Phaser positions two molecules that are related by crystallographic translational NCS. These two molecules are crystallographic-symmetry related in the original P22121 data set. I can also solve these data sets in I222 space group, with the overall Z score higher than for the P22121 data. I am uncertain, what the ‘true’ space group for some of my data sets is. Could it be that for data that process in P22121, but can be solved in I222, reflections that would indicate I222 space group were not collected? Alternatively, perhaps what I am seeing is that there is a (gradual) transition of the crystal lattice (between P22121 and I222 or vice versa), caused by variation in crystal handling/cooling or exposure to X-rays. It’s relevant to me, because in P22121 space group, a region of the molecule that is of biological interest makes NCS-related crystal contacts that are crystallographic-symmetry related in I222. Has anybody observed similar cases? I would appreciate comments. Cheers, Florian
Re: [ccp4bb] I222 - P22121 space-group ambiguity
Hi Florian, Not sure if this is helpful or not but I have a particular protein that seems to be either P22121 (with 2 molecules) or I222 (with one molecule). Not from the same drop but crystallised in similar conditions but with different small molecules bound. In many cases the crystals can be processed in both space groups but refine better in one over the other. I always thought (as the small molecules affect some loops folding on the active site in my case) that sometimes all my protein molecules had the same conformation of those loops and in other cases there were subtle differences - do you see any differences or small molecules bound asymmetrically in your P22121 cases ? Best regards Jodie From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Florian Schmitzberger [schmitzber...@crystal.harvard.edu] Sent: Monday, 13 October 2014 9:47 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] I222 - P22121 space-group ambiguity Hi everybody, I collected a number of X-ray data sets from crystals originating from the same cryst. drop. I solved the initial structure in P22121 space group by MR with Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree: 0.213/0.244. Processing of some of the other data sets with XDS/Aimless is consistent with I222 space group (resolution ~ 2.6 Ang.). I can locate one molecule. The unit-cell dimensions for I222 and the initial P22121 space groups for two of the data sets are: I222: a=87.8 b=101.18 c=123.63; P22121: a=93.34 b=105.47 c=122.98; I superposed the molecule in I222 onto one of the two located for the initially solved P22121; the orientation of the NCS-related molecule in P22121 differs from the crystallographic-symmetry related one in I222. Trying to solve this P22121 data set in I222 with MR, does not result in high Z scores, and maps do not look good. Some of the data sets that process in I222 to ~ 3 Angstr., I can also solve in P22121, locating two molecules (differences may not be that clear in this case, since the resolution is lower). Some other data sets process in P22121 with Aimless; with a substantial off-origin Patterson peak, indicating translational NCS. For these, Phaser positions two molecules that are related by crystallographic translational NCS. These two molecules are crystallographic-symmetry related in the original P22121 data set. I can also solve these data sets in I222 space group, with the overall Z score higher than for the P22121 data. I am uncertain, what the ‘true’ space group for some of my data sets is. Could it be that for data that process in P22121, but can be solved in I222, reflections that would indicate I222 space group were not collected? Alternatively, perhaps what I am seeing is that there is a (gradual) transition of the crystal lattice (between P22121 and I222 or vice versa), caused by variation in crystal handling/cooling or exposure to X-rays. It’s relevant to me, because in P22121 space group, a region of the molecule that is of biological interest makes NCS-related crystal contacts that are crystallographic-symmetry related in I222. Has anybody observed similar cases? I would appreciate comments. Cheers, Florian
Re: [ccp4bb] I222 - P22121 space-group ambiguity
It might help to look at the images and predictions. You a have serial vs integral extinctions (i.e. conditions limiting reflections are:) P 2 21 21 (Standard: P 21 21 2, btw) 0K0 : K=2N only 00L : L=2N only I222 HKL : H+K+L=2N only Alternatively you could process unmerged data with XPREP or so and look at the systematic absence violations. The lattice metric is the same for both SGs (did not understand Eleanor's remark) In principle, differences between NCS and XS of compatible metric become more distinct at higher resolution (i.e. at night, all cats are grey). Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Florian Schmitzberger Sent: Montag, 13. Oktober 2014 10:47 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] I222 - P22121 space-group ambiguity Hi everybody, I collected a number of X-ray data sets from crystals originating from the same cryst. drop. I solved the initial structure in P22121 space group by MR with Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree: 0.213/0.244. Processing of some of the other data sets with XDS/Aimless is consistent with I222 space group (resolution ~ 2.6 Ang.). I can locate one molecule. The unit-cell dimensions for I222 and the initial P22121 space groups for two of the data sets are: I222: a=87.8 b=101.18 c=123.63; P22121: a=93.34 b=105.47 c=122.98; I superposed the molecule in I222 onto one of the two located for the initially solved P22121; the orientation of the NCS-related molecule in P22121 differs from the crystallographic-symmetry related one in I222. Trying to solve this P22121 data set in I222 with MR, does not result in high Z scores, and maps do not look good. Some of the data sets that process in I222 to ~ 3 Angstr., I can also solve in P22121, locating two molecules (differences may not be that clear in this case, since the resolution is lower). Some other data sets process in P22121 with Aimless; with a substantial off-origin Patterson peak, indicating translational NCS. For these, Phaser positions two molecules that are related by crystallographic translational NCS. These two molecules are crystallographic-symmetry related in the original P22121 data set. I can also solve these data sets in I222 space group, with the overall Z score higher than for the P22121 data. I am uncertain, what the 'true' space group for some of my data sets is. Could it be that for data that process in P22121, but can be solved in I222, reflections that would indicate I222 space group were not collected? Alternatively, perhaps what I am seeing is that there is a (gradual) transition of the crystal lattice (between P22121 and I222 or vice versa), caused by variation in crystal handling/cooling or exposure to X-rays. It's relevant to me, because in P22121 space group, a region of the molecule that is of biological interest makes NCS-related crystal contacts that are crystallographic-symmetry related in I222. Has anybody observed similar cases? I would appreciate comments. Cheers, Florian
Re: [ccp4bb] I222 - P22121 space-group ambiguity
Yes, having different crystal forms in the same crystallization conditions is, while clearly uncommon, not unheard of. I had a case once where at least four different crystal forms were observed in crystals harvested from identically prepared drops. It may be that there is some major set of contacts that promote certain arrangement of protein molecules (fiber-like), and these can then be packed in multiple ways as controlled by another ser of weaker interactions. Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: Florian Schmitzberger schmitzber...@crystal.harvard.edu /divdivDate:10/13/2014 4:47 AM (GMT-05:00) /divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] I222 - P22121 space-group ambiguity /divdiv /divHi everybody, I collected a number of X-ray data sets from crystals originating from the same cryst. drop. I solved the initial structure in P22121 space group by MR with Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree: 0.213/0.244. Processing of some of the other data sets with XDS/Aimless is consistent with I222 space group (resolution ~ 2.6 Ang.). I can locate one molecule. The unit-cell dimensions for I222 and the initial P22121 space groups for two of the data sets are: I222: a=87.8 b=101.18 c=123.63; P22121: a=93.34 b=105.47 c=122.98; I superposed the molecule in I222 onto one of the two located for the initially solved P22121; the orientation of the NCS-related molecule in P22121 differs from the crystallographic-symmetry related one in I222. Trying to solve this P22121 data set in I222 with MR, does not result in high Z scores, and maps do not look good. Some of the data sets that process in I222 to ~ 3 Angstr., I can also solve in P22121, locating two molecules (differences may not be that clear in this case, since the resolution is lower). Some other data sets process in P22121 with Aimless; with a substantial off-origin Patterson peak, indicating translational NCS. For these, Phaser positions two molecules that are related by crystallographic translational NCS. These two molecules are crystallographic-symmetry related in the original P22121 data set. I can also solve these data sets in I222 space group, with the overall Z score higher than for the P22121 data. I am uncertain, what the ‘true’ space group for some of my data sets is. Could it be that for data that process in P22121, but can be solved in I222, reflections that would indicate I222 space group were not collected? Alternatively, perhaps what I am seeing is that there is a (gradual) transition of the crystal lattice (between P22121 and I222 or vice versa), caused by variation in crystal handling/cooling or exposure to X-rays. It’s relevant to me, because in P22121 space group, a region of the molecule that is of biological interest makes NCS-related crystal contacts that are crystallographic-symmetry related in I222. Has anybody observed similar cases? I would appreciate comments. Cheers, Florian
Re: [ccp4bb] I222 - P22121 space-group ambiguity
Hi Florian, When your pseudo-translation (native Patterson peak) is close to (0.5,0.5,0.5) even in p22121 you will have have most of reflections with h+k+l=2n+1 measured as weak. In your lower resolution datasets 2.6 and 3.0 A non-weak reflections can be lost in noise and your group assignment may go wrong, and all of your crystals may be P22121. Having said this, polymorphism is quite common. In a recent publication Acta Crystallogr D Biol Crystallogr. 2014 Sep 1;70(Pt 9):2430-43, Lebedev Isupov we describe a case where two crystals had similar cell parameters in different space groups a = 119.2, b = 192.5, c = 77.3 P212121 and a = 112.0, b = 192.2, c = 76.7 P21212. Both structures could be refined in the other space group at 1.8A resolution, but resulting R-frees were 8-15 % higher in the wrong space group. Both space group appeared as a result of symmetry breakdown in a supergroup A2122 (reindexed C2221). P212121 structure could also be refined in the supergroup with FreeR only 3 % higher than in the real space group. However as half of reflections had to be thrown out to reindex to A2122 even if FreeR would be equal in the supergroup and P212121 I would consider the latter correct. I would recommend to solve and refine your low resolution structures in all possible space groups and choose the one with better refinement statistics, preferring not centered one in case of equal Rfrees. Quality of density maps could be criteria in borderline cases. Cheers, Misha From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Florian Schmitzberger [schmitzber...@crystal.harvard.edu] Sent: 13 October 2014 09:47 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] I222 - P22121 space-group ambiguity Hi everybody, I collected a number of X-ray data sets from crystals originating from the same cryst. drop. I solved the initial structure in P22121 space group by MR with Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree: 0.213/0.244. Processing of some of the other data sets with XDS/Aimless is consistent with I222 space group (resolution ~ 2.6 Ang.). I can locate one molecule. The unit-cell dimensions for I222 and the initial P22121 space groups for two of the data sets are: I222: a=87.8 b=101.18 c=123.63; P22121: a=93.34 b=105.47 c=122.98; I superposed the molecule in I222 onto one of the two located for the initially solved P22121; the orientation of the NCS-related molecule in P22121 differs from the crystallographic-symmetry related one in I222. Trying to solve this P22121 data set in I222 with MR, does not result in high Z scores, and maps do not look good. Some of the data sets that process in I222 to ~ 3 Angstr., I can also solve in P22121, locating two molecules (differences may not be that clear in this case, since the resolution is lower). Some other data sets process in P22121 with Aimless; with a substantial off-origin Patterson peak, indicating translational NCS. For these, Phaser positions two molecules that are related by crystallographic translational NCS. These two molecules are crystallographic-symmetry related in the original P22121 data set. I can also solve these data sets in I222 space group, with the overall Z score higher than for the P22121 data. I am uncertain, what the ‘true’ space group for some of my data sets is. Could it be that for data that process in P22121, but can be solved in I222, reflections that would indicate I222 space group were not collected? Alternatively, perhaps what I am seeing is that there is a (gradual) transition of the crystal lattice (between P22121 and I222 or vice versa), caused by variation in crystal handling/cooling or exposure to X-rays. It’s relevant to me, because in P22121 space group, a region of the molecule that is of biological interest makes NCS-related crystal contacts that are crystallographic-symmetry related in I222. Has anybody observed similar cases? I would appreciate comments. Cheers, Florian
Re: [ccp4bb] I222 - P22121 space-group ambiguity
Hi Bernhard et al The lattice metric is the same for both SGs (did not understand Eleanor’s remark) Hmmm - well the I212121 cell and the P21221 cells you give here have different volumes, so they cant be just rearrangements of symmetry operators and non-cryst translation. Cell volume for the I222 cell = 87.8 * 101.18 * 123.63 ~= 1,098,280 Å^3 Cell volume for the P22121 cell = 93.34 * 105.47 * 122.98 ~=1,210,685 Å^3 Or ~10% different - so to me, anyway, Eleanor's remark made perfect sense. In principle, differences between NCS and XS of compatible metric become more distinct at higher resolution (i.e. at night, all cats are grey). Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Florian Schmitzberger Sent: Montag, 13. Oktober 2014 10:47 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] I222 - P22121 space-group ambiguity Hi everybody, I collected a number of X-ray data sets from crystals originating from the same cryst. drop. I solved the initial structure in P22121 space group by MR with Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree: 0.213/0.244. Processing of some of the other data sets with XDS/Aimless is consistent with I222 space group (resolution ~ 2.6 Ang.). I can locate one molecule. The unit-cell dimensions for I222 and the initial P22121 space groups for two of the data sets are: I222: a=87.8 b=101.18 c=123.63; P22121: a=93.34 b=105.47 c=122.98; I superposed the molecule in I222 onto one of the two located for the initially solved P22121; the orientation of the NCS-related molecule in P22121 differs from the crystallographic-symmetry related one in I222. Trying to solve this P22121 data set in I222 with MR, does not result in high Z scores, and maps do not look good. Some of the data sets that process in I222 to ~ 3 Angstr., I can also solve in P22121, locating two molecules (differences may not be that clear in this case, since the resolution is lower). Some other data sets process in P22121 with Aimless; with a substantial off-origin Patterson peak, indicating translational NCS. For these, Phaser positions two molecules that are related by crystallographic translational NCS. These two molecules are crystallographic-symmetry related in the original P22121 data set. I can also solve these data sets in I222 space group, with the overall Z score higher than for the P22121 data. I am uncertain, what the ‘true’ space group for some of my data sets is. Could it be that for data that process in P22121, but can be solved in I222, reflections that would indicate I222 space group were not collected? Alternatively, perhaps what I am seeing is that there is a (gradual) transition of the crystal lattice (between P22121 and I222 or vice versa), caused by variation in crystal handling/cooling or exposure to X-rays. It’s relevant to me, because in P22121 space group, a region of the molecule that is of biological interest makes NCS-related crystal contacts that are crystallographic-symmetry related in I222. Has anybody observed similar cases? I would appreciate comments. Cheers, Florian Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
Re: [ccp4bb] I222 - P22121 space-group ambiguity
I think Eleanor was looking at the cell axis in particular a and b they are off by almost 10%, hence unlikely to be identical, unless I missed something there. Jürgen .. 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: +1-410-614-4742tel:%2B1-410-614-4742 Lab: +1-410-614-4894tel:%2B1-410-614-4894 Fax: +1-410-955-2926tel:%2B1-410-955-2926 http://lupo.jhsph.edu On Oct 13, 2014, at 11:30 AM, Bernhard Rupp b...@ruppweb.orgmailto:b...@ruppweb.org wrote: It might help to look at the images and predictions. You a have serial vs integral extinctions (i.e. conditions limiting reflections are:) P 2 21 21 (Standard: P 21 21 2, btw) 0K0 : K=2N only 00L : L=2N only I222 HKL : H+K+L=2N only Alternatively you could process unmerged data with XPREP or so and look at the systematic absence violations. The lattice metric is the same for both SGs (did not understand Eleanor’s remark) In principle, differences between NCS and XS of compatible metric become more distinct at higher resolution (i.e. at night, all cats are grey). Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Florian Schmitzberger Sent: Montag, 13. Oktober 2014 10:47 To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] I222 - P22121 space-group ambiguity Hi everybody, I collected a number of X-ray data sets from crystals originating from the same cryst. drop. I solved the initial structure in P22121 space group by MR with Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree: 0.213/0.244. Processing of some of the other data sets with XDS/Aimless is consistent with I222 space group (resolution ~ 2.6 Ang.). I can locate one molecule. The unit-cell dimensions for I222 and the initial P22121 space groups for two of the data sets are: I222: a=87.8 b=101.18 c=123.63; P22121: a=93.34 b=105.47 c=122.98; I superposed the molecule in I222 onto one of the two located for the initially solved P22121; the orientation of the NCS-related molecule in P22121 differs from the crystallographic-symmetry related one in I222. Trying to solve this P22121 data set in I222 with MR, does not result in high Z scores, and maps do not look good. Some of the data sets that process in I222 to ~ 3 Angstr., I can also solve in P22121, locating two molecules (differences may not be that clear in this case, since the resolution is lower). Some other data sets process in P22121 with Aimless; with a substantial off-origin Patterson peak, indicating translational NCS. For these, Phaser positions two molecules that are related by crystallographic translational NCS. These two molecules are crystallographic-symmetry related in the original P22121 data set. I can also solve these data sets in I222 space group, with the overall Z score higher than for the P22121 data. I am uncertain, what the ‘true’ space group for some of my data sets is. Could it be that for data that process in P22121, but can be solved in I222, reflections that would indicate I222 space group were not collected? Alternatively, perhaps what I am seeing is that there is a (gradual) transition of the crystal lattice (between P22121 and I222 or vice versa), caused by variation in crystal handling/cooling or exposure to X-rays. It’s relevant to me, because in P22121 space group, a region of the molecule that is of biological interest makes NCS-related crystal contacts that are crystallographic-symmetry related in I222. Has anybody observed similar cases? I would appreciate comments. Cheers, Florian
Re: [ccp4bb] I222 - P22121 space-group ambiguity
Hi Florian, a couple of things come to my mind: a) you have to be careful in your use of XDS; if you specify space group number 18 it will use P 21 21 2 as space group, whereas you seem to use the ordering abc and call the space group P 2 21 21. (Not long ago, I tried to bring this up on this mailing list) In practice, this won't affect INTEGRATE and CORRECT, except that the list in CORRECT.LP REFLECTIONS OF TYPE H,0,0 0,K,0 0,0,L OR EXPECTED TO BE ABSENT (*) will have the wrong markers, and AVERAGE INTENSITY FOR XX REFLECTIONS WHICH SHOULD BE SYSTEMATICALLY ABSENT IS YY% OF MEAN INTENSITY will have the wrong values. And if you use XDSCONV and F2MTZ to create the MTZ file, the space group operators in the file will be _wrong_. b) For a P22121 packing that is close I222, there is a danger that only the strong reflections (those with H+K+L=2N) are indexed, which would give an apparent (wrong) space group of I222. To prevent this, (if using XDS) you should make sure to use STRONG_PIXEL not higher than 4, use a large SPOT_RANGE, inspect the list CLUSTER COORDINATES AND INDICES WITH RESPECT TO REC. LATTICE BASIS VECTORS in IDXREF.LP ( http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/IDXREF.LP ) to find whether there are half-integer indices, and to visually check predictions (XDSGUI - see http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSGUI ) presents a way to do this easily. c) According to the ITC vol A, P22121 and I222 have a subgroup-supergroup relationship so it is indeed possible that a small change in the packing can convert one to the other d) ZANUDA is the program to use in case of space-group ambiguity HTH, Kay On Mon, 13 Oct 2014 10:47:18 +0200, Florian Schmitzberger schmitzber...@crystal.harvard.edu wrote: Hi everybody, I collected a number of X-ray data sets from crystals originating from the same cryst. drop. I solved the initial structure in P22121 space group by MR with Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree: 0.213/0.244. Processing of some of the other data sets with XDS/Aimless is consistent with I222 space group (resolution ~ 2.6 Ang.). I can locate one molecule. The unit-cell dimensions for I222 and the initial P22121 space groups for two of the data sets are: I222: a=87.8 b=101.18 c=123.63; P22121: a=93.34 b=105.47 c=122.98; I superposed the molecule in I222 onto one of the two located for the initially solved P22121; the orientation of the NCS-related molecule in P22121 differs from the crystallographic-symmetry related one in I222. Trying to solve this P22121 data set in I222 with MR, does not result in high Z scores, and maps do not look good. Some of the data sets that process in I222 to ~ 3 Angstr., I can also solve in P22121, locating two molecules (differences may not be that clear in this case, since the resolution is lower). Some other data sets process in P22121 with Aimless; with a substantial off-origin Patterson peak, indicating translational NCS. For these, Phaser positions two molecules that are related by crystallographic translational NCS. These two molecules are crystallographic-symmetry related in the original P22121 data set. I can also solve these data sets in I222 space group, with the overall Z score higher than for the P22121 data. I am uncertain, what the �true� space group for some of my data sets is. Could it be that for data that process in P22121, but can be solved in I222, reflections that would indicate I222 space group were not collected? Alternatively, perhaps what I am seeing is that there is a (gradual) transition of the crystal lattice (between P22121 and I222 or vice versa), caused by variation in crystal handling/cooling or exposure to X-rays. It�s relevant to me, because in P22121 space group, a region of the molecule that is of biological interest makes NCS-related crystal contacts that are crystallographic-symmetry related in I222. Has anybody observed similar cases? I would appreciate comments. Cheers, Florian
Re: [ccp4bb] I222 - P22121 space-group ambiguity
Hi everybody, Thank you for your comments! The data sets that index in I222 tend to have shorter a and b axes. I have data sets in I222 with a=95.31 b=106 c=125.9 though (still need to look at these in detail). These axes are relatively close to those in the original P22121, which I processed and refined. Some of the P22121 data sets with strong translational NCS, which can be solved in I222 too, have dimensions of a=93.04 b=104.3 c=123.6; i.e. very similar to the original P22121 that is inconsistent with I222. The off-origin Patterson peak in the P22121 space group with trans. NCS is at 0.46, 0.50, -0.50 and at 22 % height - relative to the origin peak. This peak is also present in the originally solved P22121 (where no substantial translational NCS was flagged), with a peak height of 18 %. Cheers, Florian P.S.: As I understand, P22121 should be fine to process (and deposit in the PDB); and there is no need to reindex to HM convention P21212. On Oct 13, 2014, at 11:08 AM, Eleanor Dodson eleanor.dod...@york.ac.ukmailto:eleanor.dod...@york.ac.uk wrote: Hmmm - well the I212121 cell and the P21221 cells you give here have different volumes, so they cant be just rearrangements of symmetry operators and non-cryst translation. Do you get other sets of cell dimensions for different processing? Eleanor On 13 October 2014 09:47, Florian Schmitzberger schmitzber...@crystal.harvard.edumailto:schmitzber...@crystal.harvard.edu wrote: Hi everybody, I collected a number of X-ray data sets from crystals originating from the same cryst. drop. I solved the initial structure in P22121 space group by MR with Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree: 0.213/0.244. Processing of some of the other data sets with XDS/Aimless is consistent with I222 space group (resolution ~ 2.6 Ang.). I can locate one molecule. The unit-cell dimensions for I222 and the initial P22121 space groups for two of the data sets are: I222: a=87.8 b=101.18 c=123.63; P22121: a=93.34 b=105.47 c=122.98; I superposed the molecule in I222 onto one of the two located for the initially solved P22121; the orientation of the NCS-related molecule in P22121 differs from the crystallographic-symmetry related one in I222. Trying to solve this P22121 data set in I222 with MR, does not result in high Z scores, and maps do not look good. Some of the data sets that process in I222 to ~ 3 Angstr., I can also solve in P22121, locating two molecules (differences may not be that clear in this case, since the resolution is lower). Some other data sets process in P22121 with Aimless; with a substantial off-origin Patterson peak, indicating translational NCS. For these, Phaser positions two molecules that are related by crystallographic translational NCS. These two molecules are crystallographic-symmetry related in the original P22121 data set. I can also solve these data sets in I222 space group, with the overall Z score higher than for the P22121 data. I am uncertain, what the ‘true’ space group for some of my data sets is. Could it be that for data that process in P22121, but can be solved in I222, reflections that would indicate I222 space group were not collected? Alternatively, perhaps what I am seeing is that there is a (gradual) transition of the crystal lattice (between P22121 and I222 or vice versa), caused by variation in crystal handling/cooling or exposure to X-rays. It’s relevant to me, because in P22121 space group, a region of the molecule that is of biological interest makes NCS-related crystal contacts that are crystallographic-symmetry related in I222. Has anybody observed similar cases? I would appreciate comments. Cheers, Florian
Re: [ccp4bb] I222 - P22121 space-group ambiguity
As I understand, P22121 should be fine to process (and deposit in the PDB); and there is no need to reindex to HM convention P21212. No need to, but trivial and then in conformance with the ITC. If we have a standard listing in ITC, why not use it? Having different symbols/settings for the same SG only adds complexity to data mining without providing a tangible benefit. Ergo, non-parsimonious and fails Occam's razor which in turn follows form Bayes (Jefferys, W.H. Berger, J.O. (1991). American Scientist 80, 64-72. Sharpening Ockham's razor on a Bayesian strop). Best, BR Numquam ponenda est pluralitas sine necessitate Multitude must never be proposed without necessity
Re: [ccp4bb] I222 - P22121 space-group ambiguity
Yes, I missed the second set of cell constants and assumed Florian is talking about ambiguity in the same data set. Thx BR From: Harry Powell [mailto:ha...@mrc-lmb.cam.ac.uk] Sent: Montag, 13. Oktober 2014 12:14 To: b...@hofkristallamt.org Cc: Harry Powell; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] I222 - P22121 space-group ambiguity Hi Bernhard et al The lattice metric is the same for both SGs (did not understand Eleanors remark) Hmmm - well the I212121 cell and the P21221 cells you give here have different volumes, so they cant be just rearrangements of symmetry operators and non-cryst translation. Cell volume for the I222 cell = 87.8 * 101.18 * 123.63 ~= 1,098,280 Å^3 Cell volume for the P22121 cell = 93.34 * 105.47 * 122.98 ~=1,210,685 Å^3 Or ~10% different - so to me, anyway, Eleanor's remark made perfect sense. In principle, differences between NCS and XS of compatible metric become more distinct at higher resolution (i.e. at night, all cats are grey). Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Florian Schmitzberger Sent: Montag, 13. Oktober 2014 10:47 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] I222 - P22121 space-group ambiguity Hi everybody, I collected a number of X-ray data sets from crystals originating from the same cryst. drop. I solved the initial structure in P22121 space group by MR with Phaser locating two molecules (data to ~ 2.1 Angstr.); refined R/Rfree: 0.213/0.244. Processing of some of the other data sets with XDS/Aimless is consistent with I222 space group (resolution ~ 2.6 Ang.). I can locate one molecule. The unit-cell dimensions for I222 and the initial P22121 space groups for two of the data sets are: I222: a=87.8 b=101.18 c=123.63; P22121: a=93.34 b=105.47 c=122.98; I superposed the molecule in I222 onto one of the two located for the initially solved P22121; the orientation of the NCS-related molecule in P22121 differs from the crystallographic-symmetry related one in I222. Trying to solve this P22121 data set in I222 with MR, does not result in high Z scores, and maps do not look good. Some of the data sets that process in I222 to ~ 3 Angstr., I can also solve in P22121, locating two molecules (differences may not be that clear in this case, since the resolution is lower). Some other data sets process in P22121 with Aimless; with a substantial off-origin Patterson peak, indicating translational NCS. For these, Phaser positions two molecules that are related by crystallographic translational NCS. These two molecules are crystallographic-symmetry related in the original P22121 data set. I can also solve these data sets in I222 space group, with the overall Z score higher than for the P22121 data. I am uncertain, what the true space group for some of my data sets is. Could it be that for data that process in P22121, but can be solved in I222, reflections that would indicate I222 space group were not collected? Alternatively, perhaps what I am seeing is that there is a (gradual) transition of the crystal lattice (between P22121 and I222 or vice versa), caused by variation in crystal handling/cooling or exposure to X-rays. Its relevant to me, because in P22121 space group, a region of the molecule that is of biological interest makes NCS-related crystal contacts that are crystallographic-symmetry related in I222. Has anybody observed similar cases? I would appreciate comments. Cheers, Florian Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
