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IUCr Validation Criteria - PLATON tests

PLAT_11x : ADDSYM Tests for missed symmetry (with an expanded MISSYM (C) clone)
These tests warn for missed or possible higher (pseudo) symmetry in the structural model (i.e. based on the coordinate data). Close examination of the situation at hand is indicated in order to prove/disprove the issue (usually in combination with the reflection data).

The tests are split-up in three classes of problems:

_110 Reports on potential (pseudo/real) lattice centering or cell halving.
_111 Reports on potential additional (pseudo/real) inversion centres.
_112 Reports on potential additional (pseudo/real) rotation axes and mirrors.

Failure of each of these tests results in an ALERT Level B.

Note: Disordered atoms are not taken into account in the tests.

 PLAT_16x : Tests for missing s.u. on coordinates

Positional parameters for all non-hydrogen atoms in general positions
are checked for the presence of a non-zero s.u. on them.
This includes parameters fixed to fix the origin in polar space groups
which is no longer necessary when refinement is done with modern programs
(e.g. SHELXL, XTAL).

_161 Missing or Zero su (esd) on x-coordinate.
_162 Missing or Zero su (esd) on x-coordinate.
_163 Missing or Zero su (esd) on x-coordinate.

Failure of these tests results in an ALERT Level C.

 PLAT_202 Test for isotropic non-hydrogen atoms in anion/solvent (small moiety)

This test reports on isotropically refined atoms in small moieties (usually
anions or solvent)

Failure of this test results in an ALERT Level C.

 PLAT_211 Test for NPD ADP's in main residue(s)

This test reports on non-positive definite (i.e. complex and unrealistic)
anisotropic displacement parameters in the main residue.

Failure of this test results in an ALERT Level A.

 PLAT_212 Test for NPD ADP's in small moieties (solvent/anions)

This test reports on non-positive definite (i.e. complex and unrealistic)
anisotropic displacement parameters in small moieties (solvent/anion).

Failure of this test results in an ALERT Level B.

 PLAT_213 ADP maximum/minimum ratio test for main residue

The maximum and minimum main axis ADP ratio (Angstrom Units) is tested
for the main residue. Large values may indicate unresolved disorder.

IF ratio > 5.0 THEN issue ALERT Level A.
IF ratio > 4.0 THEN issue ALERT Level B.
IF ratio > 3.0 THEN issue ALERT Level C.

 PLAT_214 ADP maximum/minimum ratio test for small moiety

The maximum and minimum main axis ADP ratio (Angstrom Units) is tested
for the minor residue(s). Large values may indicate unresolved disorder.

IF ratio > 6.0 THEN issue ALERT Level A.
IF ratio > 5.0 THEN issue ALERT Level B.
IF ratio > 4.0 THEN issue ALERT Level C.

 PLAT_301, _302 : Detection of Disorder

Atom sites that are not fully occupied are counted. A large fraction of
disordered atoms may be both a signal for serious structure determination
problems or less reliable/interesting results. A distinction is made
for 'solvent molecules of less interest' (_302) and the
'main components' (_301)

For PLAT_301
IF disorder > 50% THEN issue ALERT Level A.
IF disorder > 25% THEN issue ALERT Level B.
IF disorder > 0% THEN issue ALERT Level C.

For PLAT_302
IF disorder > 0% THEN issue ALERT Level C.

 PLAT_305 Test for 'Isolated' Hydrogen atoms

This test reports on hydrogen atoms that are not on bonding distance to
any atom.

Failure of this test results in an ALERT Level A.

 PLAT_310 Test for 'Too close' (symmetry related) full weight atoms.

This test identifies (very) short contacts between atoms that only becomes
apparent after the application of symmetry on the primary coordinate set.

Failure of this test results in an ALERT Level A.
PLAT_320, _321 : Checks on Hybridisation of C atoms

This test is split up in two sections: the main molecule (_320) and
solvent molecules (_321).

The test attempts to assign one of three hybridisations to C atoms:
sp, sp2 or sp3 on the basis of the angles around C. In this way, missing
H atoms or two many H-atoms on a carbon atom should be detected.

Failure of this test results in an ALERT Level C.

 PLAT_350 : _373 : Test for Short/Long Bonds as compaired with standard values

Large deviations from generally accepted values may indicate model
problems, overrefinement etc.

Default (X-Ray) values are from SHELXL (X-H) and
Ladd & Palmer, Structure Determination by Xray Crystallography (1985).

Note: C4-C3 indicates a bond between an atom with 4 bonds and one with 3 bonds.

Conjugated systems may cause some 'false alarm' messages.

_352 Short N - H 0.87 Ang.
_353 Long N - H 0.87
_354 Short O - H 0.82
_360 Short C4 - C4 1.54
_361 Long C4 - C4 1.54
_362 Short C4 - C3 1.52
_363 Long C4 - C3 1.52
_364 Short C4 - C2 1.46
_365 Long C4 - C2 1.46
_367 Long C? - C? 1.50
_368 Short C3 - C3 1.34
_369 Long C3 - C3 1.34
_370 Short C3 - C2 1.31
_371 Long C3 - C2 1.31
_372 Short C2 - C2 1.25
_373 Long C2 - C2 1.25

IF discrepancy > 0.3 Ang. THEN issue ALERT Level A.
IF discrepancy > 0.2 Ang. THEN issue ALERT Level B.
IF discrepancy > 0.1 Ang. THEN issue ALERT Level C.

 PLAT_420 : Test for D-H without acceptor

Potential hydrogen bond donors are checked for the presence of suitable
acceptors using commonly used (Jeffrey) H-bond criteria. As a general rule
there should be an acceptor for each donor. Exceptions are very rare for
O-H and more common for -NH and -NH2. A common error is an -OH on a
calculated position pointing in the wrong direction.

Failure of this test results in an ALERT Level C.

 PLAT_601, _602 : Solvent Accessible Void(s) Test(s)

Crystal structures in general do not contain large solvent accessible
voids in the lattice. Most structures loose their long-range ordening
when solvent molecules leave the crystal. Only when the remaining network
is strongly bonded (e.g. zeolites and some hydrogen bonded networks) the
crystal structure may survive.

Residual voids in a structure may indicate the omission of (disordered)
density from the model. Disordered density may go undetected when smeared
since peak search programs are not designed to locate maxima on density
ridges. The presence or absence of residual density in the void may be
veryfied on a printed/plotted difference Fourier map or with PLATON/SQUEEZE.

Voids of 40 Ang**3 may accommodate H2O. Small molecules such as Tetrahydro
Furane have typical volumes in the 100 to 200 Ang**3 range.


_601 : This test reports the volume of the largest solvent accessible void
in the structure.

IF void > 200 THEN issue ALERT Level A.
IF void > 100 THEN issue ALERT Level B.
IF void > 30 THEN issue ALERT Level C.

_602 : This test reports on a void, too large for the current PLATON version
for more detailed analysis.

Failure of this test results in an ALERT Level C.