PROC-NAME: REFLT03 Type_1/3/4

PURPOSE: To check that _reflns_number_total is close to that expected for the cell volume, symmetry and theta max.

PROCEDURE:

CALCULATE

S = SIN [_diffrn_reflns_theta_max] / _diffrn_radiation_wavelength

NREF = The number of the reflections in the SYMMETRY-UNIQUE portion of reciprocal space out to a maximum of S. All symmetry absent reflections have been removed from this count.

NREFRAT = _reflns_number_total / NREF

NREF% = NREFRAT * 100

NFRIED = MAX ( _reflns_number_total - NREF, 0)

NFDRAT = NFRIED / NREF

TEST_1 : Type_1

In the calculation of NREF the maximum and minumum h,k,l indices in the in the unque portion of reciprocal space are saved. These are compared with the _diffrn_reflns_limit_ values in the CIF. If the estimated maximum h,k,l values do not match either the CIF _max or the absolute _min values issue a General ALERT

?? "ALERT: Expected hkl max differ from CIF values"

The maximum (or minimum) limits of h, k and l given in the CIF do not correspond with those caclculated using the theta(max) value stated under _diffrn_reflns_theta_max.

Check that theta(max) has been given correctly. If so, it may be that the h,k,l index limits set during the data collection did not correspond correctly with the limits required to ensure that at least all possible unique reflections up to the specified theta(max) were collected. If one or more of the index limits was set to a too small value, truncation of the data will have occurred and the data should be recollected. This problem sometimes occurs, especially with older diffractometers, when the index limits and theta(max) must be set independently by hand and the operator forgets to check both settings.

TEST_2 : Type_3 (centrosymmetric), Type_1 (non-centrosymmetric)

Test the completeness of the reflection count in the symmetry unique portion of reciprocal space.

IF NREF%

< 85 issue ALERT A

?? "Alert A: < 85% complete (theta max?)"

< 90 issue ALERT B

?? "Alert B: < 90% complete (theta max?)"

< 95 issue ALERT C

?? "Alert C: < 95% complete"

The total number of symmetry-unique reflections, including all reflections considered to be "unobserved", but excluding systematically absent reflections, should be given under _reflns_number_total. If Friedel-related reflections are being treated as independent observations in order to utilise the effects of anomalous dispersion, _reflns_number_total should correspond with the total number of these independent reflections.

The expected number of unique reflections is calculated from your reported theta(max). You should first check that theta(max) has indeed been reported correctly.

It is essential that, as far as possible, at least all possible unique reflections have been recorded up to the chosen theta(max). Severe deficiencies in this regard should be rectified by recollecting the data.

If you do not know why your data are incomplete, it can sometimes be instructive to examine the reflection file by using the ASYM-VIEW option of plaTON (requires the SHELXL format .hkl or .fcf file). This will highlight the missing reflections in each layer of the data. Missing reflections that occur in strips or inner regions of the layers suggest that an incorrect data collection strategy was used or that there was some other problem with the data collection. E.g. incorrect h,k,l limits causing truncation in one or more directions, premature termination of the data collection, loss of X-rays during part of the data collection. One accidental cause of incompleteness is to choose the wrong axis to scan completely with monoclinic space groups (e.g. collecting +h, +/-k, +l reflections when b is the unique axis).

Another reason for having incomplete data can be that your (old) data reduction program is discarding reflections with negative intensity, so that only those with positive intensity are retained in the data set and reported under _reflns_number_total. In this case, you should update or replace your data reduction program so that this does not occur.

If you are using a serial diffractometer (scintillation counter), there is usually no reason that the data should not be virtually 100% complete and severe incompleteness should be investigated carefully. Low temperature devices can sometimes be a hindrance, but should not lead to a large fraction of incomplete data.

With CCD detectors, one must ensure that the data collection strategy is sufficient to cover all unique reflections. An additional scan set at a different chi or omega setting may be required to ensure that the data set is complete.

For diffractometers with only one circle (e.g. the fixed phi circle on the Stoe IPDS and Mar Research IP systems, data completeness can be more problematic. One method for mimimising incompleteness is to ensure that the crystal is mounted such that a crystal axis is NOT coincident with the phi axis (i.e. make sure your crystals are mounted in a skew orientation).

People who use CCD or IP detectors may find that just the high angle reflections are incomplete. This occurs with rectangular apertures because the corners of the detector will record to higher angles that the mid points of the sides. In such cases it will be found that the data are essentially 100% complete at a lower theta value. This information should be incorporated into the CIF by correctly filling out the following two data items which specify the theta value at which the data are essentially 100% complete and the actual completeness at this theta value:

_diffrn_reflns_theta_full

_diffrn_measured_fraction_theta_full

One means of obtaining estimates for the above two items is to use the ACTA instruction in SHELXL, together with its optional parameter. If a value is specified for 2theta on this instruction, this value will be used to correctly fill in the above two entries in the CIF. This does not truncate the data during refinement.

Example:

We have measured to theta(max) = 28.0 deg. with 92% completeness,

but the data are virtually 100% complete to 26.3 deg.

Using ACTA 52.6 will produce the following in the CIF:

_diffrn_reflns_theta_max??????? 28.0

_diffrn_measured_fraction_theta_max??? 0.920

_diffrn_reflns_theta_full????? ??26.3

_diffrn_measured_fraction_theta_full??? 0.997

If the space group is centrosymmetric also test if the expected reflection count is exceeded (perhaps because symmetry absent or equivalent reflections were mistakenly counted). Type_3

IF NREF%

> 115 issue ALERT A

?? "Alert A: > 15% excess reflns - sys abs data present?"

> 110 issue ALERT B

?? "Alert B: > 10% excess reflns - sys abs data present?"

> 105 issue ALERT C

?? "Alert C: > 5% excess reflns - sys abs data present?"

The total number of symmetry-unique reflections, including all reflections considered to be "unobserved", but excluding systematically absent reflections, should be given under _reflns_number_total. If Friedel-related reflections are being treated as independent observations in order to utilise the effects of anomalous dispersion, _reflns_number_total should correspond with the total number of these independent reflections.

The expected number of unique reflections is calculated from your reported theta(max). You should first check that theta(max) has indeed been reported correctly.

Having excess numbers of reflections is an indication that you have not or have incorrectly merged symmetry-equivalent reflections, or that you have included the systematically absent reflections in your count of unique reflections.

Check for typographical errors and/or that you have merged the equivalent reflections correctly before refinement.

An exception to this requirement may occur if data from a non-merohedrally twinned crystal is employed, as this may result in more than one entry in the reflection file for a given set of h,k,l indices (e.g. data read into SHELXL with HKLF 5). As a result, more reflections may be used in the refinement than the apparent number of unique reflections.

A second exception might be if you deliberately choose not to merge symmetry equivalent reflections before the refinement. This procedure is not recommended and its use should be specifically mentioned under _publ_section_exptl_refinement.

(http://journals.iucr.org/services/cif/checking/REFLT_03.html)

例：REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is

??????????? correct. If it is not, please give the correct count in the

??????????? _publ_section_exptl_refinement section of the submitted CIF.

?????????? From the CIF: _diffrn_reflns_theta_max?????????? 25.00

?????????? From the CIF: _reflns_number_total?????????????? 6219

?????????? Count of symmetry unique reflns???????? 3846

?????????? Completeness (_total/calc)??????????? 161.70%

?????????? TEST3: Check Friedels for noncentro structure

??? ???????Estimate of Friedel pairs measured????? 2373

?????????? Fraction of Friedel pairs measured???? 0.617

?????????? Are heavy atom types Z>Si present??????? yes

警告原因：Friedel pairs數(shù)目有問題。

解決策略：給出合理解釋即可。