Deal all, Sorry for the long post. I have a data set obtained from a crystal produced after incubating a protease with a protein which is mostly composed by an antiparallel beta sheet. I have tried numerous approaches to solve it, and failed. Molecular replacement using Phaser, and the protease or the protein as a template yields no solution. However, molecular replacement using only part of the beta sheet yields LLG=320 TFZ==28.0 (see below).
The apparently good data extends to 1.9 A, as processed by XDS, and the space group is P1 (pointless agree). XDS info below: SPACE_GROUP_NUMBER= 1 UNIT_CELL_CONSTANTS= 44.43 72.29 77.30 97.802 89.939 101.576 a b ISa 9.647E-01 3.176E-03 18.07 RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 1.90 24890 19149 23814 80.4% 58.1% 63.7% 11482 0.77 82.2% 63.8* 3 0.694 492 total 163756 125884 146938 85.7% 10.6% 10.8% 75744 3.78 15.0% 99.0* -3 0.761 5834 Xtriage in Phenix 1.16-3549 gives me all green lights (print below), suggesting the data presents no twinning, no translational NCS, no ice rings and is not anisotropic. http://fullonline.org/science/phenix_xtriage_green.png Molecular replacement in Phaser yields single solutions like: Solution annotation (history): SOLU SET RFZ=3.0 TFZ=* PAK=0 LLG=29 RFZ=2.8 TFZ=8.8 PAK=1 LLG=310 TFZ==27.6 LLG=320 TFZ==28.0 SOLU SPAC P 1 SOLU 6DIM ENSE ensemble1 EULER 293.6 27.7 288.7 FRAC -0.02 0.02 0.02 BFAC -6.03 SOLU 6DIM ENSE ensemble1 EULER 294.0 27.9 288.8 FRAC -0.37 0.02 0.02 BFAC -6.52 SOLU ENSEMBLE ensemble1 VRMS DELTA -0.1983 RMSD 0.49 #VRMS 0.21 or partial solutions like: Partial Solution #1 annotation (history): SOLU SET RFZ=3.7 TFZ=* PAK=0 LLG=32 RFZ=2.8 TFZ=13.0 PAK=0 LLG=317 TFZ==30.2 LLG=331 TFZ==30.5 RFZ=2.4 TFZ=7.2 PAK=0 LLG=464 TFZ==18.5 RFZ=2.7 TFZ=5.7 PAK=1 LLG=501 TFZ==6.8 LLG=509 TFZ==6.6 SOLU SPAC P 1 SOLU 6DIM ENSE ensemble1 EULER 85.4 153.0 138.5 FRAC -0.01 -0.00 -0.00 BFAC -12.30 SOLU 6DIM ENSE ensemble1 EULER 86.2 153.2 139.5 FRAC -0.36 -0.01 -0.01 BFAC -9.16 SOLU 6DIM ENSE ensemble1 EULER 83.8 152.3 135.9 FRAC -0.00 0.00 -0.25 BFAC 1.52 SOLU 6DIM ENSE ensemble1 EULER 191.2 109.1 39.3 FRAC -0.27 -0.01 0.22 BFAC 10.18 SOLU ENSEMBLE ensemble1 VRMS DELTA -0.0447 RMSD 0.49 #VRMS 0.44 However, after 1 refinement round in Phenix_Refine (Final: r_work = 0.4881 r_free = 0.5009) I got densities that are part good and part bad, and if I delete the bad parts and refine again, the good parts become bad. Please check the prints: http://fullonline.org/science/good_part_of_density.png http://fullonline.org/science/bad_part_of_density.png What is the explanation for these molecular replacement results? What else should I try? Arcimboldo takes 2 days+ to run and yields no good solution. Thank you! Regards, Napo ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1