Hi Mario, well Eleanor beat me to it but here goes anyway - please do consider examining all possibilities within spacegroups for P orthorhombic. When there are more than one molecule per ASU, NCS can mimic CS and in certain cases there appears to be a 21 screw axis when the true symmetry along that axis is a pure 2 fold. As an example, see 2IQI – lengthy searching for Se sites in P212121 failed. We then performed searches in P222 P21212 and P2221 in each circular permutation of the cell edges (abc, cab, bca) and found the right arrangement (cab in P21212).
good luck, jbb From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Mario Tyago Murakami Sent: Thursday, July 18, 2019 11:28 AM To: [email protected] Subject: Re: [ccp4bb] Se-SAD phasing Dear Andy, Clemens and Michal The solution for orthrombic SG is very clear. P1 indexing results in a very similar Unit cell parameters without appreciable deviations in angles <0.1degrees. It seems more likely the problem pointed by Andy of a lot of sites. I will try all the suggestions and hope to come back soon with good news. Thanks Mario Em 18 de jul de 2019 11:44, THOMPSON Andrew <[email protected]<mailto:[email protected]>> escreveu: Dear Mario The data seem very good but you are looking for an awful lot of sites. Keep trying with SHELX, but there are some keywords that you might use which may help (see extract from SHELX doc). This worked for me for a couple of structures with > 100 sites. You should also try with and without Patterson seeding. You may need many thousand trials…. I would also start with the data cutoff somewhere between 3.5 - 4 A (to get rid of anisotropy) . You could also try manually modifying the Emin value to use just your strongest signal. Don’t expect the solution to come out easily - you may have to try different shelx runs for days before getting a single solution. At the same time, you really do need to be absolutely certain of the space group ……any tests you can do Good luck Andy For large selenomethionine substructures (which behave more like equal atom ab initiostructure solution of small molecules) it may be worth increasing the number of Pattersonpeaks used for the Patterson seeding (e.g. PATT 200; the default is 100) and adding theinstructions WEED 0.3 (random omit maps) and SKIP 0.5 (uranium atom removal). Thelatter two are the defaults when PLOP is present but are switched off by default if PLOP isabsent. When PATS is used, WEED produces a much smaller additional improvement in thehit ratio than when PATS is absent. For small substructures (<10 sites), WEED and SKIP cando more harm than good by eliminating too many correct sites at once. De : CCP4 bulletin board [mailto:[email protected]] De la part de Mario Tyago Murakami Envoyé : jeudi 18 juillet 2019 16:19 À : [email protected]<mailto:[email protected]> Objet : [ccp4bb] Se-SAD phasing Dear all, I am trying to solve the phases of the following SeMet data, but so far unsuccessfully. Suggestions are very welcome. Please see below some details about the case. The statistics below is from a merged data from different kappas of the same crystal to increase redundancy. We used the fixed energy 12675 eV since the fluorescence detector was not working at the used beamline to get best energy values for this crystal. Xtriage did not indicate any crystallographic pathology, except moderate anisotropy. The unit cells parameters are 118.72 151.82 167.05 90.000 90.000 90.000 (P212121) containing from 8 to 12 molecules in the asymmetric unit. The protein has ~28.5 kDa and 10 Met residues, excluding those from the N- and C-termini, probably with low occupancy. Thus, something 80 to 120 scatterers are expected. Phenix_anomalous_signal indicates a probability of 99% to solve it and the anomalous signal is theoretically in a very good range. I have tried SHELXD with different resolutions and number of sites. I have also used Hyss. But all attempts failed. Thanks in advance Mario [cid:[email protected]] Aviso Legal: Esta mensagem e seus anexos podem conter informações confidenciais e/ou de uso restrito. Observe atentamente seu conteúdo e considere eventual consulta ao remetente antes de copiá-la, divulgá-la ou distribuí-la. Se você recebeu esta mensagem por engano, por favor avise o remetente e apague-a imediatamente. Disclaimer: This email and its attachments may contain confidential and/or privileged information. 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