Sde 2656

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	===CCP4 phaser===		===CCP4 phaser===
	*create polyalanine model from 1V19 (CCP4)		*create polyalanine model from 1V19 (CCP4)
-	*running Phaser	+	*Phaser gave a solution
	<pre>		<pre>
	SpaceGroup of Solution:  R 3 :H		SpaceGroup of Solution:  R 3 :H

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Revision as of 06:15, 4 November 2009

Contents 1 Data Integration & Reduction 2 MR (Phaser) 2.1 CCP4 phaser 2.2 Phenix.automr 2.3 Phenix.autobuild

Data Integration & Reduction

• Use CCP4i & Mosflm
• 10/14/2009 native data: successfully integrated, merged and scaled

MR (Phaser)

• 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

CCP4 phaser

• create polyalanine model from 1V19 (CCP4)
• Phaser gave a solution

   SpaceGroup of Solution:  R 3 :H

   SINGLE solution

   Solution written to PDB file: 
   /Users/igchoi/Desktop/2009.x-ray/sde2656/sde2656_6.1.pdb
   Solution written to MTZ file: 
   /Users/igchoi/Desktop/2009.x-ray/sde2656/sde2656_6.1.mtz
   Solution log-likelihood gain:  111.652
   Solution annotation (history):  RFZ=5.8 TFZ=5.5 PAK=0 LLG=34 RFZ=4.6 TFZ=9.5 PAK=0
   LLG=112 LLG=112

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

• Thankabouts
  • how about using HM (homology model)?
  • superimpose HM into best solution
  • use C-alpha only model
  • try Autobuild with these models

Phenix.autobuild

• Going on to AutoBuild with this solution (it took about 24 hrs)

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

• The model was partial (~50 residues in C-term missing)