wwPDB validation report of PDB entry 3SON

Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)

1. THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE STRAIN CLONED (ATCC 19115 / 4b / Li 2) DIFFERS FROM THE STRAIN SEQUENCED IN THE DATABASE REFERENCE (serotype 4b strain F2365). DNA SEQUENCING OF THE CLONED CONSTRUCT SHOWS AN ISOLUCINE AT POSITION 121 INSTEAD OF A VALINE. THE ISOLUCINE AT POSITION 121 IS SUPPORTED BY THE ELECTRON DENSITY.

1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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 FOR THE
REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
4. SOLVENT MOLECULES WERE EXCLUDED FROM THE AUTOMATIC ASSIGNMENT
OF THE TLS GROUPS. 5. THE DIFFRACTION DATA SHOW MEROHEDERAL
TWINNING WITH TWIN LAW "-H, K, -L". THE REFINED TWIN FRACTION
WAS 0.26. THE R-FREE TEST SET REFLECTIONS WERE CHOSEN AT RANDOM
WITH THE TWIN LAW INCLUDED. 6. BOTH SODIUM AND CALCIUM ARE PRESENT
IN THE CRYSTALLIZATION SOLUTION / PROTEIN BUFFER. CALCIUM WAS
MODELED BASED ON A SLIGHTLY BETTER FIT TO THE DENSITY BUT
THE SITE COULD BE MIXED NA AND CA. 7. THE RAMACHANDRAN OUTLIER
A60 IS IN A LOOP WITH WEAK ELECTRON DENSITY.

Crystal structure of a putativel NUDIX hydrolase (LMOf2365_2679) from Listeria monocytogenes str. 4b F2365 at 1.70 A resolution

ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION

The largest off-origin peak in the Patterson function is 5.22% 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)