Re: [ccp4bb] strange unit cell
You could try putting this into the Zanuda server http://www.ysbl.york.ac.uk/YSBLPrograms/ which will search for possible correct spacegroups given the coordinates and structure factors. There are however no reasons why you can't have a pseudo-cubic monoclinic lattice, however unlikely it is. Best wishes, Graeme On 25 October 2013 01:55, 유상헌 s...@snu.ac.kr wrote: Hi everyone, ** ** Recently I’ve got a protein crystal and I did indexing and scaling with a cubic space group (unit cell 104.115 104.115 104.115 90.0 90.0 90.0). But a Rmerge value was too high (around 0.5-0.6). So, I tried lower symmetry space groups and I successfully solved the structure with a space group P21 (Rwork/Rfree: 0.22/0.27). However, there was one strange fact. The unit cell of the P21 was 104.209 104.225 104.254 90.000 89.967 90.000. I’m confused with this fact that a, b, and c of the unit cell are almost same, and in addition, the beta angle is too close to 90. I didn’t do refinement with a twin option. So, is the space group correct? Is there anyone who know this case? ** ** Thanks, ** ** Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture Life Sciences Seoul National University Seoul 151-921, KOREA ** ** ** **
[ccp4bb] AW: [ccp4bb] strange unit cell
Dear Sangheon, there is no law that forbids P21 crystals to have a~b~c and beta~90°. It only does not happen very often. So your solution can be correct. You may want to analyze your crystal packing with ccp4 program Zanuda, to see if a higher symmetry space group could be used. Best regards, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von ??? Gesendet: Freitag, 25. Oktober 2013 02:56 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] strange unit cell Hi everyone, Recently I've got a protein crystal and I did indexing and scaling with a cubic space group (unit cell 104.115 104.115 104.115 90.0 90.0 90.0). But a Rmerge value was too high (around 0.5-0.6). So, I tried lower symmetry space groups and I successfully solved the structure with a space group P21 (Rwork/Rfree: 0.22/0.27). However, there was one strange fact. The unit cell of the P21 was 104.209 104.225 104.254 90.000 89.967 90.000. I'm confused with this fact that a, b, and c of the unit cell are almost same, and in addition, the beta angle is too close to 90. I didn't do refinement with a twin option. So, is the space group correct? Is there anyone who know this case? Thanks, Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture Life Sciences Seoul National University Seoul 151-921, KOREA
Re: [ccp4bb] strange unit cell
Dear Sangheon, you don't say which cubic space group you tried, perhaps you tried the wrong one? Did Pointless indicate a clear preference? Between P23 and P213 for instance you can tell by systematic absences along h (if they were collected ok), but between I23 and I213 the only option is to try both and see if one or the other leads to a good solution. In any case, in principle having P21 with beta near 90 and a nearly equal to b and c is rare, but possible. Greetings, Mark Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 25 Oct 2013, at 02:55, 유상헌 wrote: Hi everyone, Recently I’ve got a protein crystal and I did indexing and scaling with a cubic space group (unit cell 104.115 104.115 104.115 90.0 90.0 90.0). But a Rmerge value was too high (around 0.5-0.6). So, I tried lower symmetry space groups and I successfully solved the structure with a space group P21 (Rwork/Rfree: 0.22/0.27). However, there was one strange fact. The unit cell of the P21 was 104.209 104.225 104.254 90.000 89.967 90.000. I’m confused with this fact that a, b, and c of the unit cell are almost same, and in addition, the beta angle is too close to 90. I didn’t do refinement with a twin option. So, is the space group correct? Is there anyone who know this case? Thanks, Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture Life Sciences Seoul National University Seoul 151-921, KOREA
Re: [ccp4bb] strange unit cell
Hi Sangheon As others have said, there is nothing that stops a cell being monoclinic with those cell dimensions - indeed, there is nothing stopping it being triclinic, orthorhombic or tetragonal either (or even rhombohedral, for those of us who like to describe it with non-hexagonal axes). What *is* important is the symmetry of the reciprocal lattice; looking at projections of the reciprocal lattice along the major axes (i.e. a*, b* or c*) using a tool like hklview or viewhkl (both of which are in ccp4 6.4.0) should be sufficient to demonstrate whether you really have the higher symmetry. On 25 Oct 2013, at 01:55, 유상헌 wrote: Hi everyone, Recently I’ve got a protein crystal and I did indexing and scaling with a cubic space group (unit cell 104.115 104.115 104.115 90.0 90.0 90.0). But a Rmerge value was too high (around 0.5-0.6). So, I tried lower symmetry space groups and I successfully solved the structure with a space group P21 (Rwork/Rfree: 0.22/0.27). However, there was one strange fact. The unit cell of the P21 was 104.209 104.225 104.254 90.000 89.967 90.000. I’m confused with this fact that a, b, and c of the unit cell are almost same, and in addition, the beta angle is too close to 90. I didn’t do refinement with a twin option. So, is the space group correct? Is there anyone who know this case? Thanks, Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture Life Sciences Seoul National University Seoul 151-921, KOREA Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
[ccp4bb] strange unit cell
Hi, I tried to find out a correct space group using the program Zanuda. Surprisingly, Zanuda suggested a space group P42212 but not P21 and cubic ones. The unit cell of P42212 was 104.240 104.240 104.209 90.00 90.00 90.00. The number of molecules in an AU was 1, while there were 4 molecules in an AU of P21, and after refinement, R values were 0.199/0.247. I think it seems like a correct space group. So, I’m going to carry out re- processing. Thank you for all your help. Best regards, Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture Life Sciences Seoul National University Seoul 151-921, KOREA
[ccp4bb] strange unit cell
Hi everyone, Recently I’ve got a protein crystal and I did indexing and scaling with a cubic space group (unit cell 104.115 104.115 104.115 90.0 90.0 90.0). But a Rmerge value was too high (around 0.5-0.6). So, I tried lower symmetry space groups and I successfully solved the structure with a space group P21 (Rwork/Rfree: 0.22/0.27). However, there was one strange fact. The unit cell of the P21 was 104.209 104.225 104.254 90.000 89.967 90.000. I’m confused with this fact that a, b, and c of the unit cell are almost same, and in addition, the beta angle is too close to 90. I didn’t do refinement with a twin option. So, is the space group correct? Is there anyone who know this case? Thanks, Sangheon Yu Rm. 1053 Bldg. 200 School of Agricultural Biotechnology College of Agriculture Life Sciences Seoul National University Seoul 151-921, KOREA
