You need to try both P61 22 and P6522 with the Se sites changed fron
x,y,z to -x,-y,-z. The anom differences can be explained by either
solution. But maybe these programs automatically check both hands?
Eleanor Dodson
Ethayathulla Abdulsamath wrote:
hi BertThank you for your reply. Your are right about the values for your Pattersons and NatFourier, but the systematic absences and pointless suggested me to be P6122 and according to mathews coeff i get 1 molecule with Vm= 2.06 solvent= 40.42. My protein has two SeMet sites so i searched for two sites. I have just pasted few reflections which showed me P61. then based on pointless i tried P6122 0 0 3 1.9 1.8 0.5 1.8 0 0 4 0.0 2.7 1.1 2.5 0 0 5 0.4 3.5 -0.5 3.3 0 0 6 427.5 33.6 399.9 30.3 0 0 7 14.3 5.9 4.0 4.8 0 0 8 1.5 5.8 -4.4 6.3 0 0 9 10.8 6.7 -2.1 7.5 0 0 10 7.0 7.3 1.5 7.2 0 0 11 -3.8 9.3 -2.7 8.4 0 0 12 201.7 19.1 198.6 19.8 0 0 13 22.5 9.6 12.5 9.9 0 0 14 2.9 10.7 0.0 8.5 0 0 15 -21.0 12.6 1.4 12.1 0 0 16 -1.6 12.6 10.8 12.3 0 0 18 6649.0 474.7 6423.4 460.5 0 0 19 -4.6 16.5 -8.5 15.1 0 0 20 -44.1 17.0 -16.3 16.7 0 0 21 34.6 20.7 61.8 18.5 0 0 22 -16.7 12.5 -15.4 15.9 0 0 23 -46.2 18.7 -35.9 18.2 pointless resultsBest Solution space group P 61 2 2 Reindex operator: [h,k,l] Laue group probability: 1.000 Systematic absence probability: 0.963 Total probability: 0.963 Space group confidence: 0.949 Laue group confidence 1.000thank youEthayathullaOn Thu, 21 May 2009 19:44:27 -0400 "Bert Van Den Berg" wrote Re: [ccp4bb] MAD phasing Hi, My guess is that you don’t have the right space group. The values for your Pattersons and NatFourier are way too low, especially the NatFourier you would like to be at least 2-3 or so. In your assigned space group, do you have a reasonable value for the matthews coefficient? Is there NCS? Are you finding the expected number of Se sites? Again, I would try to investigate alternative SGs. Also it would be a good idea to take the sites and refine them with SHARP. Good luck, Bert On 5/21/09 6:38 PM, "Ethayathulla Abdulsamath" wrote: hello I am have a MAD dataset collected upto 2.3A but anomalous signal is upto 3.5A. The dataset is in P6 and based on pointless and absences it is P6122. Overall Rlin/rsym is (0.07/ 0.06). the overall redundancy is 10. I have two Se peaks, i used solve/resolve to find those peaks. I used datasets from 3.5 to 20A to find peaks i got two good peaks of occ (1.4 & 0.92). I did analyze_solve and refined those peaks. Then i tried resolve to autobuild and phasing but it didnt work. The r-factor FC vs FP is 0.40 and FOM 0.6, although the results looks promising i couldnt find proper phasing using phenix, resolve.autobuild. i tried phenix.autosol also but it didnt work. how can i check the peaks are real. can anybody suggest me how do I proceed further and what r the mistakes i am doing.. Thank you Ethayathulla FROM SOLVE Site x y z occ B -- PEAK HEIGHT -- 1 0.386 0.986 0.050 1.449 60.000 23.82 2 0.623 0.997 0.046 0.921 60.000 22.11 Summary of scoring for this solution: -- over many solutions-- -- this solution -- Criteria MEAN SD VALUE Z-SCORE Pattersons: 0.129 0.500 0.279 0.299 Cross-validation Fourier: 4.83 2.62 41.8 14.1 NatFourier CCx100: 3.28 1.24 3.93 0.521 Mean figure of meritx100: 0.00 7.16 53.5 7.48 Correction for Z-scores: -10.5 Overall Z-score value: 11.9 RESOLVE results CORRECTED OVERALL FIGURE OF MERIT OF PHASING: 0.61 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR: 0.39 * * ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP: 0.61 * * NOTE: The fraction from prior will be roughly proportional to * Overall average CC: 0.5423778 Results of wilson scaling of model Fc to Fo : Scale on I to apply to Fc = 1.934 B-value to apply to Fc= 1.971 Overall R-factor for FC vs FP: 0.404 for 3288 reflections Leaving out 1 reflections with FC=0 and correcting R-factor to 0.4036375 from 0.4035717 as only 99.96960 % of the reflections are ok Writing overall R-factor 0.4036375 to "resolve.rfactor" ################################################### A.S.Ethayathulla,Ph.D. Department of Biophysics All India Institute of Medical Sciences Ansari Nagar New Delhi-110029 India. ###################################################
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A.S.Ethayathulla,Ph.D.
Department of Biophysics
All India Institute of Medical Sciences
Ansari Nagar
New Delhi-110029
India.
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