Sde 2656
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*create polyalanine model from 1V19 (CCP4) | *create polyalanine model from 1V19 (CCP4) | ||
*running Phaser | *running Phaser | ||
| + | <pre> | ||
| + | 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 | ||
| + | </pre> | ||
===Phenix.automr=== | ===Phenix.automr=== | ||
Revision as of 06:15, 4 November 2009
Contents |
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)
- running Phaser
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)
