wwPDB validation report of PDB entry 3PJ0

THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.ELECTRON DENSITY INDICATES THAT LYS 207 ON THE FOUR SUBUNITS IN THE ASYMMETRIC UNIT ARE COVALENTLY ATTACHED TO PYRIDOXAL-5'- PHOSPHATE; THERFORE THESE RESIDUES WERE MODELED AS 2-LYSINE (3- HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)(LLP). 6. 2-METHYL-2,4-PENTANEDIOL (MPD,MRD), CHLORIDE (CL), AND SODIUM IONS FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE. 7. THE PROGARM QFIT THAT AUTOMATICALLY IDENTIFIES AND MODELS DISCRETE HETEROGENEITY IN ELECTRON DENSITY MAPS WITH A A CONVEX OPTIMIZATION ALGORITHM WAS IMPLEMENTED DURING REFINEMENT TO MODEL ALTERNATE CONFORMATIONS.

Crystal structure of a putative L-allo-threonine aldolase (lmo0305) from Listeria monocytogenes EGD-E at 1.80 A resolution

CRYSTAL PACKING INDICATES THAT A DIMER IS AN OLIGOMERIZATION STATE.

The analyses of the Patterson function reveals a significant off-origin peak that is 31.21 % of the origin peak, indicating pseudo-translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 1.1496e-03.

structure factor analysis and validation
geometric validation package for ligand chemistry in protein x-ray structures
20191225.v01 (using entries in the PDB archive December 25th 2019)