wwPDB validation report of PDB entry 2OPK

Single crystal Si(111) bent (horizontal focusing)

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. ONE CHLORIDE ION AND FIVE GLYCEROL MOLECULES FROM CRYSTALLIZATION
WERE MODELED INTO THE STRUCTURE.
5. ELECTRON DENSITY WAS OBSERVED NEAR THE PUTATIVE ACTIVE SITE
RESIDUE 103 ON EACH SUBUNIT. THESE DENSITIES WERE MODELED AS AN
UNKNOWN LIGAND (UNL).
6. UNINTERPRETABLE ELECTRON DENSITY IS OBSERVED BETWEEN THE SIDECHAINS
OF GLU 54 AND TYR 48 OF THE C-SUBUNIT. THIS DENSITY WAS NOT MODELED.
7. RESIDUE 111 IN SUBUNIT A, RESIDUES 1 TO 2 AND 111 IN SUBUNIT C ARE
DISORDERED AND NOT BUILT IN THIS MODEL.

CRYSTAL STRUCTURE OF A PUTATIVE MANNOSE-6-PHOSPHATE ISOMERASE (REUT_A1446) FROM RALSTONIA EUTROPHA JMP134 AT 2.10 A RESOLUTION

SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

The largest off-origin peak in the Patterson function is 3.66% 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)