From CSBLwiki
Data Integration & Reduction
- Use CCP4i & Mosflm
- 10/14/2009 native data: successfully integrated, merged and scaled
- Use Phenix at panpyro cluster <- shortening your computation time
# swissmodel superimposed to 1V19 MR solution
# run autobuild in cluster (panpyro)
phenix.autobuild ../MR.1_copy.mtz ../swissAB.pdb seq_file=../sde2656.fas run_command="qsub -q infi" background=False nproc=5 nbatch=5 >& job.log &
phenix.automr ../pointless_sde2656_1_001_scala1-2.6A.mtz ../MR2_1V19_polyALA.pdb seq_file=../sde2656.fas copies=2 identity=25 run_command="qsub -q infi" background=False nproc=5 nbatch=5 >& job.log &
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)
