Bijvoet centre for biomolecular research, vakgroep kristal- en structuurchemie, university of utrecht
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- 9.3 PLATON - ANALYSE Menu WinGX v1.64
- 11. SQUEEZE, An effective cure for the disordered solvent syndrome in crystal structure refinement. 11.1 General
- 11.2 Implementation and Use
- 9.3 PLATON - ANALYSE Menu
- 11.4 Interpretation of the results
- 12 PLATON in the WinGX implementation
9.3 PLATON - ANALYSE Menu
Chapter. 9.3 PLATON 37 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)
_305 Test for 'Isolated' Hydrogen atoms This test reports on hydrogen atoms that are not on bonding distance to any atom. _306 & _311 Test for 'Isolated' Oxygen atoms This test reports on oxygen atoms that are not within bonding distance to any other atom in the structure. A common reason may be that no hydrogen atoms are given for a water molecule. Alert _306 is issued for full weight atoms, _311 otherwise. _307 Test for 'Isolated' Metal atoms This test reports on metal atoms that are not bonded or at coordination distance of other atoms. Isolated ions are very unusual (or non-existent ?) _308 Test for single bonded metal atoms This test reports on single bonded (coordinated) metal atoms/ions. This represents a very unusual situation. There are literature examples where such a 'single bonded metal' was shown to be a halogen.
_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. _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 too many H-atoms on a carbon atom should be detected. _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. _350 Short C - H Reference Xray : 0.96 Ang _351 Long C - H 0.96 _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 9.3 PLATON - ANALYSE Menu
Chapter. 9.3 PLATON 38 _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 _380 Check for Methyl Moiety refinement This test alerts for possible unrefined CH3 moieties. (E.g. AFIX 33 instead of AFIX 137 etc. within the SHELXL realm) _390, _391 Test for unusual CH3 geometry. _390 Reports on unusual X-C-H Angles _391 Reports on unusual H-C-H Angles Methyl moieties easily refine to poor geometries when refined in a poorly defined electron densityi or due to orientational disorder. If so, refinement with relevant con-/restraints should be considered. _410, _413 : Tests for Short Intra and Intermolecular H...H Contacts Short intermolecular H..H contacts may indicate incorrectly determined structures (i.e. wrong symmetry, missed translation symmetry, wrong position with reference to the symmetry elements, hydrogen atoms on atoms where there should not be any etc..). Short intramolecular contacts may arise when H-atoms are in (false) calculated positions. Short intramolecular contacts may also be a sign for a false structure with the molecule sitting on a site with improper site symmetry (e.g. '2' instead of '-1') which may happen when a lattice translation is missed. Short contacts are defined using a van der Waals radius of 1.2 Angstrom. For intermolecular contacts, an alert is generated for contacts less than 2.4 Angstrom. For intramolecular contacts alerts are generated for contacts less than 2.0 Angstrom. Shorter intramolecular contacts may make sense for crowded configurations, in particular when hydrogen atoms are calculated in idealised positions. _412 & _413 report on short H .. H contact involving CH3 H-atoms. Those positions are often optimal when in calculated position. _416 : Test for short intra D-H .. H-D contacts Such contacts may be related to disordered of misplaced H-atoms. _417 : Test for short inter D-H .. H-D contacts Such contacts may be related to disordered of misplaced H-atoms. _420 : Test for D-H without acceptor 9.3 PLATON - ANALYSE Menu
Chapter. 9.3 PLATON 39 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. _430 : Test for short intermolecular D..A distances This test alerts for possibly missed hydrogen bonds as indicated by short (i.e. shorter than sum of the van der Waals radii - 0.2) donor - acceptor distances. _431 : Test for short intermolecular Hl...D distances
This test reports on short intermolecular halogen .. donor/acceptor atom- type distances. _432 : Test for short intermolecular distances This test reports on short intermolecular atom-type distances falling in anather class than alerts _430, _431.
_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 water. Small molecules such as tetrahydrofuran 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. _602 : This test reports on a void, too large for the current PLATON version for more detailed analysis. _701, _702, _703 Check for consistency of derived geometry and coordinates The bond distances, angles and torsion angles given in the CIF are cross- checked with corresponding values calculated from the coordinates. Alerts are set at 1,2 and 3 sigma deviation levels. Note: Default s.u.'s are used where no su given (e.g. for C-H) In general, all differences should be within the associated su. Small differences may arise from rounding. Very large deviation (or zero distance) normally indicate incorrectly specified symmetry operations on the associated atoms, or 'cut-and-pasting' of incompatible CIF's. _704 Check for consistency of contact distance geometry and coordinates 9.3 PLATON - ANALYSE Menu
Chapter. 9.3 PLATON 40 Intermolecular contacts listed in the CIF are checked against the coordinates in the CIF. Alerts are set at 1,2 and 3 sigma deviation levels. _705, _706, _707, _708 Check of H-Bond geometry against coordinates Hydrogen-Bond data (D-H, H..D, D..A, D-H..A) listed in the CIF are checked. Alerts are set at 1,2 and 3 sigma deviation levels. _710 Check for linear torsions Torsion angles specified in the CIF are checked for the 'linear variety' where one or both of the 1-2-3 and 2-3-4 bond angles are close to 180 Deg. SHELXL97 will generate those 'torsions' for molecules containing linear moieties (E.g. metal-C=O). _711 to _718 Inconsistent labels When labels are found on geometry items (bonds, angles etc.) that are not in the coordinate list, and alert _71n is issued, related to alert _70n. _721, _722, _723, _724 Check for consistency of derived geom. and coordinates Same as _701, _702, _703, _704, but for distances, angles and torsions without su (esd). Difference is tested in terms of Angstroms and Degrees. _725, _726, _727, _728 Check of H-Bond geometry against coordinates Same as _705, _706, _707, _708, but for distances and angles without su (esd). Differences are tested in terms of Angstrom and Degrees. _731 to _738 Check on 'Comparable' reported and calculated s.u. Same as _701 to _708 but for reported and calculated s.u.'s (Ratio) This range of checks should warn for erroneous rounding: E.g. 105.5(19) to 105.5(2) 105.0(5) to 105(5) etc. _741 to _748 Check for missing s.u.'s on bonds, angles, torsions An alert in this series generally indicates a missing s.u. on the reported bond, angle, torsion. _751 to _758 Check for senseless s.u.'s on Bonds, Angles, Torsions Alerts are issued for constrained bonds, angles, torsions (i.e. with the R flag in the CIF or of the type X-Y-X' = 180 where Y is on an inversion center.
_761, _762 Check for presence of X-H bonds and X-Y-H or H-Y-H angles The CIF should also contain those data. _763, _764 Check for too few or too many non X-H Bonds in CIF _780 Check for Connected Atom SET 9.3 PLATON - ANALYSE Menu
Chapter. 9.3 PLATON 41 Atoms given in a CIF should form a 'connected set', i.e. no symmetry operations are needed to get atoms in a bonding position. A connected set of atoms is not needed for the refinement (unless hydrogen atoms are to be added at calculated positions). Geometry listings (bonds,angles,torsions & H-bonds) become unwieldy for non-connected atom sets. _790 Check for Residue Centres to be within the Unitcell bounds Unless for a good reason, molecular species should be transformed (by symmetry and/or translation) so that their centres of gravity are close to or within the unitcell bounds. This is a strict rule for the main species. Deviations from this general rule are smaller additional species when relevant for intermolecular interactions with the main species.
See P. v.d. Sluis & A.L. Spek. Acta Cryst. (1990), A46, 194 The current version of SQUEEZE has been designed, dimensioned and tested for small moiety structures containing disordered solvent molecules of the type toluene, CH 2 Cl
, tetrahydrofuran, water, methanol etc.. Anions may be treated in the same way. However, take care of the problem of uncertainty of charge balance. Large voids currently require significant computing in the stage where the size and shape of the solvent accessible void is determined. All calculations are done in the triclinic system (data are expanded automatically when appropriate). Reflection data and FFT-array are stored in memory i.e. large structures (and high symmetry) may require large amounts of memory (change parameter NP21, that defines the available scratch area, globally to a larger value). 11.2 Implementation and Use SQUEEZE as implemented in the program PLATON should be compatible with small-moiety structure refinement usage of the program SHELXL-97. The program is used as a filter. Input files are : • name.HKL SHELX file (HKLF type 4) • name.RES SHELX file (complete set of refined model parameters, including hydrogen atoms but excluding any dummy atoms used to describe the disorder region)
Invoke the program by giving, on the prompt >> (or click on the menu) the instruction: CALC SQUEEZE The result will be in two files: • name.LIS a listing file giving details of the calculations • name.HKP: a modified reflection file against which the ordered structure parameters can be refined (the solvent contribution has been eliminated from the reflection data.)
9.3 PLATON - ANALYSE Menu
Chapter. 9.3 PLATON 42 In order to run SHELXL-97 on the 'solvent-free' Fo 2 data you will need to rename the file name.HKP to name.HKL In order to get an .FCFstyle file (Fo 2 + Fc 2 (model + solvent)) you will need to run PLATON with the option CALC FCF
Final R-values are reported on the basis of the WGHT parameters in the name.RES file. There will be a difference in reflection count as compared with the SHELXL-run due to the differing number of surviving 'observed' reflections. The procedure (starting from the original reflection data) can be repeated using the newly refined parameters when desired. This may define a 'refined' void area. However, there will be rarely a need to repeat the procedure. The 'difference-map' improvement potential of this technique has been demonstrated for small molecule structures. The technique should also work for protein data. However, this has not been tested by us as yet with PLATON/SQUEEZE. Current design features may cause problems when tried. A directory containing test-examples is in (the PLATON ftp site at) /pub/unix/platon/TEST/SQUEEZE_TEST.'
• The record length of the name.HKP file has been increased above 80 to accommodate additional data (the exact details are not fixed) • The SHELXL-TWIN instruction is not available as yet in PLATON • PLATON internally calculates structure factors for the model given in the shelxl.ins file. • The solvent contribution to the structure factors is taken as 'error-free'. This means that the 'solvent-free' Fo 2 keep their original su's (esd's) • The method relies heavily on the quality of the low-order reflections. The dataset should be as complete as possible. Systematic errors may hamper the quality of the results. Current conditions for applicability are 1. Reasonable data-resolution (say 25 degrees Mo) 2. Structure of the known part completed with H-atoms 3. No more than 26 'voids' in the unit-cell 4. Disorder density should be well outside the van der Waals surface of the known structure 5. The area to be SQUEEZED should not be too large (say less than ~30% of the unit-cell volume.
1. A successful application of SQUEEZE will show the following results: • A new hkl-file against which a satisfactory refinement of the discrete model can be done (purpose: good geometry, good R-value) • Smooth convergence of the SQUEEZE iteration. • Significant improvement of the R-value in low resolution data. (see table at the end of the listing file). • The number of electrons reported to be found in a void is close to that expected for the assumed solvent. • The difference map peaklist should not contain significant peaks outside the VOID areas. • Peaklist is given in the file name.SQZ
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Chapter. 9.3 PLATON 43
2. Problems are indicated when: • Convergence is unstable • A large number of reflections left out during the iteration process (This may be well indicative for problems with the data, and should be checked for). 3. A report on the use of SQUEEZE should always state for each (significant) independent void:
• Where the void is (i.e. x,y,z) • Its volume • The number of electrons recovered.
The version of PLATON in WinGX is virtually identical to the UNIX workstation version, except that System S is not available (it is too UNIX specific). The major differences concern the input and output files. To maintain the normal WinGX file naming protocols, the ASCII listing file is renamed as PLATON.LST while the input files are generally created automatically. In normal operation, a temporary file called name.SPF is created by reading, in the following order, the SHELXL.LST (to try and obtain errors on the coordinates), the
the program may abort. The first thing to check is whether the SHELXL.LST file is from a refinement which has terminated normally - if not delete this file. The output name.HKP files are also usually renamed depending on the operation carried out The program is ALWAYS run in locked mode because of this renaming procedures. The hypertext help functions exactly as in the UNIX version. . Document Outline
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