wwPDB validation report of PDB entry 3LN3

Flat collimating mirror, toroid focusing mirror

1.THIS 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. 2.THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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.SULFATE (SO4) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED IN THE SOLVENT STRUCTURE. 4.ENDOGENOUS NICOTINAMIDE ADENINE DINUCLEOTIDE (NAD), WHICH IS THE EXPECTED COFACTOR FOR THIS PROTEIN, HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE. THE NAD SHOWS SOME DISORDER IN THE STRUCTURE. 5.(4R)-2-METHYLPENTANE-2,4-DIOL (MRD), WHICH MAY BE A SUBSTRATE MIMIC, HAS BEEN MODELED IN THE PUTATIVE ACTIVE SITE BASED ON THE ELECTRON DENSITY. HOWEVER, IT IS POSSIBLE THAT THIS MAY BE SOME OTHER COMPOUND. 6.THE PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION PRIOR TO CRYSTALLIZATION. LYSINE 84 APPEARS TO HAVE BEEN PROTECTED FROM REDUCTIVE METHYLATION AND WAS MODELED AS LYSINE. ALL OTHER LYSINES HAVE BEEN MODELED AS N-DIMETHYL-LYSINE (MLY).

Crystal structure of Putative reductase (NP_038806.2) from MUS MUSCULUS at 1.18 A resolution

CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

The largest off-origin peak in the Patterson function is 8.35% of the height of the origin peak. No significant pseudotranslation is detected.

20191225.v01 (using entries in the PDB archive December 25th 2019)

structure factor analysis and validation

geometric validation package for ligand chemistry in protein x-ray structures