wwPDB validation report of PDB entry 3MBJ

Single crystal Si(111) bent monochromator (horizontal focusing)

putative phosphomethylpyrimidine kinase (BT_4458) from Bacteroides thetaiotaomicron VPI-5482 at 2.0 A resolution (orthorhombic form with pyridoxal)

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. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SULFATE IONS (SO4) AND 2-METHYL-2,4-PENTANEDIOL (MPD & MRD) MOLECULES FROM CRYSTALLIZATION ARE MODELED IN THE STRUCTURE. 5. AN IMIDAZOLE MOLECULE (IMD) FROM THE PROTEIN BUFFER IS MODELED IN THIS STRUCTURE. 6. ZINC IONS (ZN) AND A CHLORIDE ANION (CL) FROM THE CRYSTALLIZATION DROP ADDITIVE ARE MODELED IN THE STRUCTURE.

Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution (rhombohedral form)

The largest off-origin peak in the Patterson function is 4.24% of the height of the origin peak. No significant pseudotranslation is detected.

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)