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Contents 1 AMD 2 Structure determination 2.1 Native set 2.1.1 MR 2.1.2 CCP4 2.1.3 Phenix automr 2.2 Se-Met Set 2.2.1 Data 1 2.3 Phenix automr

AMD

• aryl acylamidase
• 496 aa + 6 histag = 502 aa
• MW = 53,240.8 (496) + 840.8 (6His), pI=5.42
• Met = 15 sites

Structure determination

• Data collected@PLS
• Cryo condition is critical
  • Annealing crystals in the liquid nitrogen stream - use a credit card

Native set

• diffracted to 1.8A
• CCP4i (mosflm): Data processing

Lattice point group: P 4 2 2 (no. 89)
Lattice unit cell: 76.31. 76.31 214.82 90.00 90.00 90.00

MR

• Closest PDB

1. 2F2A A: 30% id., aligned 3-457
2. 3H0L A: 25% id., aligned 5-476
3. 2GI3 A: 26% id., aligned 12-465
4. 3A1K A: 33% id., aligned 151-499
5. 3A2P A: 34%, 7-231
6. 1M21 A: 29%, 38-482
7. 2WJ1 A: 31%, 77-255

CCP4

• Matthews coefficient = 2.90 (1 molecule/asu)

Phenix automr

• what you should prepare - materials
• qsub option = 'qsub -q infi'
• LLG값이 100이상이면 solution

   Top Peaks With Clustering
   -------------------------
   #       Rank of the peak after rescoring search points
   (#)     Rank of the peak before rescoring search points
   LLG     Log-Likelihood Gain
   Z-Score Number of standard deviations of LLG above the mean
   FSS     Fast Search Score

   You requested peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
   There was 1 site over 75% of top
   The sites over 75% are:
   #     (#)   Frac X Frac Y Frac Z   LLG   Z-score Split #Group    raw/top 
   1     1      0.112  0.629  0.356  +91.94   11.61     0      1 278.89/278.89

• automr tutorial

Se-Met Set

Data 1

• cannot be processed in Mosflm
• HKL2000 (by SY Lee)
  • R-value was not good
  • used 2.8-50A data (R-value?)

Phenix automr

• commandline@panpyro

phenix.automr data=out1.mtz coords=1.pdb identity=0.3 seq_file=seq.dat   \
input_seq_file=seq.dat copies=1 run_command='qsub -q infi' background=False   \
nproc=2 nbatch=2 

• data= (.sca or .mtz; have scaled)
• coords= (model pdb file; single chain)
• identity= (% identity between model and target)
• seq_file= (amino acid sequence; fasta format)
• copies= (# of molecules in ASU; obtained from matthews's coefficient calculation)
• run_command= (define only when the calculation is made using linux cluster (panpyro))
• download sample data

Best solution on cycle: 13    R/Rfree=0.32/0.41