TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / OXIDOREDUCTASE / ArnB Transferase
Function / homology
Function and homology information
UDP-4-amino-4-deoxy-L-arabinose aminotransferase / UDP-4-amino-4-deoxy-L-arabinose aminotransferase / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / pyridoxal phosphate binding / response to antibiotic / metal ion binding Similarity search - Function
UDP-4-amino-4-deoxy-L-arabinose-oxoglutarate aminotransferase, ArnB / DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase Similarity search - Domain/homology
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→58.82 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.82 / Stereochemistry target values: ML Details: Lattice-translocation disorder correction notes: Native Patterson shows three off-origin peaks. Strongest one with vector (0.4029 0.50000.618), second one (0.1953 0.000 0.7638), and third ...Details: Lattice-translocation disorder correction notes: Native Patterson shows three off-origin peaks. Strongest one with vector (0.4029 0.50000.618), second one (0.1953 0.000 0.7638), and third one at (0.2092 0.5000 0.8536), corresponding to 1X Td, 2X Td and 3X Td, respectively, with relative intensities to orgin peak of ~65%, ~30% and 8.5% (CCP4 fft used; phenix.xtriage showed even higher values like 73%, 34% and 10%, most likely due to grid sampling difference), respectively. Peak 1 and 2 are mostly targeted. Peak 1 corresponds to tNCS too, so after correction it is lowered but not eliminated. Peak 2 eventually gone. Final Rwork and Rfee went down to 19.81% and 21.99%,respectively. Without correction, the Rwork and Rfree, with best try, are paused at 31.38% and 33.83%, respectively.
Rfactor
Num. reflection
% reflection
Rfree
0.2199
5787
5 %
Rwork
0.1981
-
-
obs
0.1992
115703
99.65 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL