Sde 2656

From CSBLwiki

Revision as of 09:55, 3 November 2009 (view source) Igchoi (Talk | contribs) (→Phenix.autobuild) ← Older edit		Revision as of 09:56, 3 November 2009 (view source) Igchoi (Talk | contribs) (→Phenix.autobuild) Newer edit →
Line 23:		Line 23:
	model=AutoBuild_run_1_/cycle_best_9.pdb \		model=AutoBuild_run_1_/cycle_best_9.pdb \
	rebuild_in_place=True \		rebuild_in_place=True \
-	seq_file=/home/igchoi/tools/epmr/mr2/sde2656.seq	+	seq_file=sde2656.seq

---

Revision as of 09:56, 3 November 2009

MR

• get MR models (PDB homologs) - 1TZ6_A, 2V78_A, 1TYY_A, 2DCN_A, 3IQ0_A, 1V19_A (Top 6 PDBs) by Psi-blast
• superimpose them into 1TZ6_A (make multiple models & compare those structures) by UCSF chimera

Phenix.automr

• 1st trial: use multiple models
  • it didn't give any good solution
• 2nd trial: try each model looking for the best solution
  • 1V19A gave best solution
  • resolution 4-20 was enough to find the solution
  • judgement: LLG>100, Z-score>7
  • our solution was almost at edge

Solution annotation (history):  RFZ=5.2 TFZ=4.6 PAK=0 LLG=35 RFZ=5.6 TFZ=7.7 PAK=1
   LLG=92 LLG=92
Log likelihood gain for solution MR: 92.0433

Phenix.autobuild

• Going on to AutoBuild with this solution now

phenix.autobuild \
 data=AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz \
 model=AutoBuild_run_1_/cycle_best_9.pdb \
 rebuild_in_place=True \
 seq_file=sde2656.seq


SOLUTION  CYCLE     R        RFREE     BUILT   PLACED 
 1         2      0.37        0.44      575       328
 2         3      0.32        0.40      503       235
 3         4      0.28        0.35      515       359
 4         5      0.27        0.34      529       388
 5         6      0.26        0.33      545       400
 6         7      0.25        0.31      551       407
 7         8      0.25        0.31      555       411
 8         9      0.24        0.30      552       446