Several checks need to be performed totally up-front because if something has gone wrong with the symmetry data or with the interpretation of amino acids or ligands, then many subsequent validation options won't work optimally.
WHAT_CHECK has a whole series of X-ray specific validation options. Many of these options give warnings and errors that are immediately clear to crystallographers but that might be hard to explain to other users of PDB files. Most of the X-ray specific messages are Warnings, and those that are Errors do often not influence the biological conclusions albeit that hydrogen bond optimization, bump checking, ion-type determinations, etc., will probably not function very well. The box below lists a series of these Warnings:
C-unique setting for "B 2" Cell is non-standard Triclinic cell with mixed acute and obtuse angles Non-triclinic cell with acute angle Unconventional orthorhombic cell Class of space group could be incorrect Class of conventional cell differs from CRYST1 cell Unconventional cell on CRYST1 Nonstandard space group setting Matthews Coefficient (Vm) high Scale and cryst1 differ slightly Symmetry information inconsistent New symmetry found Conventional cell is pseudo-cell |
But the following messages represent Errors, and it is not always a priori clear what influence these errors have had (or will still have) on the structure determination, structure validation, or on the usage of the structure to answer biomedical questions.
Cell contains short vector CRYST1 cell represents wrong crystal class Invalid space group Matthews Coefficient (Vm) very high Matthews Coefficient (Vm) too low The SCALE matrix gives a left handed axis system Scale matrix represents wrong crystal class Negated value in scale matrix The SCALE matrix is nonstandard Value in first row of scale matrix mistyped Value in second row of scale matrix mistyped Value in third row of scale matrix mistyped Inconsistent SCALE and CRYST1 cards Determinant of MTRIX is incorrect (MTRIX is phased out...) Determinant of MTRIX is not exactly 1.0 MTRIX is not a pure rotation matrix |
In many of the cases listed in the boxes above, WHAT_CHECK doesn't give a note if things seem to be correct. It happens so very often, though, that atoms are observed too close to a symmetry axis that we decided to write a note if the problem has not been observed.
If you run into any of these errors then you either are a crystallographer and you know what to do, or you will need to be careful reading the rest of the validation report as these are typically the types of errors that can put WHAT_CHECK in a state of confusion.
The Matthews coefficient, Vm, relates to the density of the cell in terms of macromolecule volume versus water volume. Normal Vm coefficients range from 1.5 for tightly packed crystals to 4.0 for very loosely packed, watery crystals. Numbers outside this range are occasionally seen, but not often, and not far outside this range.
If the Vm value listed is very weird, then the cause most often is the Z value on the CRYST1 card. The note below is the text about the CRYST1 card, extracted from the PDB documentation.
NOTEIn summary, if something goes wrong with the Vm calculations, consult a seasoned crystallographer.