wwPDB validation report of PDB entry 1M06

Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame

Atomic structure of the single-stranded bacteriophage phix174

Atomic structure of the degraded procapsid particle of the bacteriophage G4.

DNA packaging intermediates of the bacteriophage phix174

icosahedral asymmetric unit, std point frame

This bacteriophage has a single stranded DNA genome of 6087 nucleotides. In the asymmetric unit the authors can see non protein density which they have attributed to the ssDNA. This density is weak and there is no density for the base portion of the nucleotides because the sequence will be different in all the 60 subunits in the virus. The sugar-phosphate portion of a nucleotide was built in with no particular sequence in mind and is thus not necessarily a 10mer of CYTs. There is no particular connectivity associated with the DNA. It is all just fragments. The numbering of the nucleotides is irrellevant since they are all identical, have no bases, and the authors can see only about 10% of the entire genome. Only nucleotides 1, 2, 3, and 4 are linked, the others are not linked.

Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography

The largest off-origin peak in the Patterson function is 9.32% 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)