Or perhaps there is only 1 copy and more solvent than you expect? This is not that uncommon.
On 20 Sep 2014 12:09, Randy Read <[email protected]> wrote: > > Just to add to what Herman said: > > The statistics are good for placing the domain represented by ensemble 1 > (TFZ=14.3) and the first copy of the domain represented by ensemble 2 > (TFZ=11.9), but not for the two possible solutions for placing the second > copy of ensemble 2 (TFZs of 4.5 and 4.7). So it’s possible that only the > placement of the first two components is correct. If you turn on symmetry in > coot, do those two domains come together to form a sensible whole protein? > If so, you could try using that composite model to look for more copies of > the whole protein (keeping in mind Herman’s point about the possible numbers > of copies). > > That said, it’s going to be a challenge to finish up the structure rebuilding > and refinement when you have limited resolution and relatively low sequence > identity starting models. With 3-fold or greater NCS, averaging would help a > great deal (2-fold helps somewhat but is less powerful); otherwise, you’re > likely to need some additional phase information. > > Best wishes, > > Randy Read > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > Wellcome Trust/MRC Building Fax: +44 1223 336827 > Hills Road E-mail: > [email protected] > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > On 19 Sep 2014, at 10:33, Veerendra KUMAR (IMCB) > <[email protected]> wrote: > > > Dear CCP4 members, > > > > Recently I have collected native data at 3.3 A resolution. The structure of > > the protein should have two domains. The structure of c terminal domain > > from homologous (30 seq similarity) is known. I took n terminal domain from > > another homologous protein. I ran the phaser using these two ensembles and > > got the following solutions. > > # [No title given] > > SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 > > LLG=259 TFZ==7.0 RFZ=4.0 TFZ=4.5 PAK=24 LLG=207 TFZ==7.4 > > SOLU SPAC I 41 3 2 > > SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 > > 0.92422 BFAC -7.23070 > > SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 > > 0.10135 BFAC 1.81823 > > SOLU 6DIM ENSE ensemble2 EULER 351.235 68.606 254.802 FRAC 0.64931 0.81795 > > 0.27592 BFAC 5.82534 > > SOLU ENSE ensemble1 VRMS 1.157 > > SOLU ENSE ensemble2 VRMS 1.540 > > SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 > > LLG=259 TFZ==7.0 RFZ=2.7 TFZ=4.7 PAK=19 LLG=202 > > SOLU SPAC I 41 3 2 > > SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 > > 0.92422 BFAC -7.23070 > > SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 > > 0.10135 BFAC 1.81823 > > SOLU 6DIM ENSE ensemble2 EULER 41.452 118.850 315.630 FRAC 0.61025 0.05816 > > 1.60902 BFAC 5.47988 > > SOLU ENSE ensemble1 VRMS 1.157 > > SOLU ENSE ensemble2 VRMS 1.540 > > > > The TFZ score 14.3 suggests a solution. Then I did refinement using Ploy > > Ala phaser model. The R values are 0.590/0.62. I use the map to build the > > model in Buccaneer but it did not build anything. > > > > Is the pahser solution correct? Why are the R values so high despite the > > good TFZ score? Any suggestions are greatly appreciated. > > > > Thank you > > > > Veerendra > > > > > > > > Note: This message may contain confidential information. If this Email/Fax > > has been sent to you by mistake, please notify the sender and delete it > > immediately. Thank you.
