Crystallography Open Database

Information card for entry 2008177

2008176 << 2008177 >> 2008178

Preview

Coordinates	2008177.cif
Original IUCr paper	HTML

Structure parameters

Chemical name	Dichloro[1-(thiomethyl)-2-(diphenylphosphino)ethane]palladium(II)
Formula	C15 H17 Cl2 P Pd S
Calculated formula	C15 H17 Cl2 P Pd S
SMILES	[Pd]1(Cl)(Cl)[S](CC[P]1(c1ccccc1)c1ccccc1)C
Title of publication	A dichloropalladium(II) complex with a mixed-donor bidentate ligand: dichloro[2-(diphenylphosphino)-1-(methylthio)ethane-<i>P</i>,<i>S</i>]palladium(II)
Authors of publication	Adnan S. Abu-Surrah; Kristian Lappalainen; Martti Klinga; Markku Leskelä; Hamdallah A. Hodali; Bernhard Rieger
Journal of publication	Acta Crystallographica Section C
Year of publication	1999
Journal volume	55
Journal issue	2
Pages of publication	188 - 190
a	11.36 ± 0.003 Å
b	12.237 ± 0.002 Å
c	11.717 ± 0.002 Å
α	90°
β	93.63 ± 0.03°
γ	90°
Cell volume	1625.5 ± 0.6 Å³
Cell temperature	193 ± 2 K
Ambient diffraction temperature	193 ± 2 K
Number of distinct elements	6
Space group number	14
Hermann-Mauguin space group symbol	P 1 21/n 1
Hall space group symbol	-P 2yn
Residual factor for all reflections	0.05
Residual factor for significantly intense reflections	0.037
Weighted residual factors for all reflections	0.077
Weighted residual factors for significantly intense reflections	0.073
Goodness-of-fit parameter for all reflections	1.03
Goodness-of-fit parameter for significantly intense reflections	1.07
Diffraction radiation wavelength	0.71073 Å
Diffraction radiation type	MoKα
Has coordinates	Yes
Has disorder	No
Has F_obs	No

Version history

Revision	Date	Message	Files
176435 (current)	2016-02-14	cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries from ranges 1, 2.	2008177.cif
134621	2015-04-02	The 'cif_fix_values' script with an option '--fix-only-weighting-scheme' and 'cif_filter' script were run over CIF files which included an incorrect value of the data item '_refine_ls_weighting_scheme'. Read the log for more details. There were more than 18k CIF files with values to modify. Usually these incorrect values include comment with formulas, but values of this data item must be an enumerator. The script creates new data item '_refine_ls_weighting_details' to store these comments with formulas, and writes the enumerator 'calc' as a value of data item '_refine_ls_weighting_scheme'. There exists some exceptions in the script.	2008177.cif
130086	2015-01-23	cod/ (robertas@burundukas) The 'cif_fix_values' program was applied to CIFs that have generated the validation messages containing tag '_exptl_crystal_density_meas'. 16946 CIFs had a values that were perceived as 'not measured' and they were changed to '?'. The total of 17089 CIFs was changed. Those that were not corrected by 'cif_fix_values' were reformatted by the parser (e.g. a doi tag was moved to another place). The processing command was: mysql -u cod_reader -h www.crystallography.net cod -e \ 'select distinct codid from validation \ where message like \ "%tag%_exptl_crystal_density_meas'\''%"' -NB \ \| xargs -i sh -c 'cif_fix_values {} \ \| cif_filter --add-cif-header {} \ \| sponge {}'	2008177.cif
91933	2013-12-28	cif/ (saulius@koala.ibt.lt) Adding DOIs that could be assigned unambiguously to the range 2x CIFs.	2008177.cif
32112	2012-02-03	cif/: committing an update of 45+ thous files, with information appended from the originals.	2008177.cif
26848	2011-09-28	cif/2/, hkl/2/, html/ Reorganising CIFs of the range 2* into the "prefix-directory" tree.	2008177.cif
26029	2011-09-17	cif/2/ Reverting changes of revision 25271: ( cd cif/2/; svn merge -r25271:25270 . ) The problem was that the reprocessed files from IUCr, although were more complete, "resurrected" data errors that were corrected in the previous recisions. The additional data that have been extracted during the reprocessing will have to be merged without overwriting the existing values in COD files, except some explicit and controlled cases (such as publication titles and chemical names).	2008177.cif
25271	2011-09-10	cif/2/ Adding reporocessed IUCr CIFs for the years 1980-2010. The CIFs now contain more complete bibliography, substance names, correctly unfolded text fields (using the CIF line unfolding protocol), explicitely set cell angles, and _cod_data_source_block fields.	2008177.cif
5310	2011-01-02	cif/ Running cif_fix_enum with the core CIF dictionary on COD ranges 2, 8 and 9. Range 9 remained unchanged, and in ranges 2 and 8 there were 17309 modified files, most changes were fixes enumerator case.	2008177.cif
966	2010-01-30	cif/ Adding _cod_database_code tags to all COD entries. Adding tag description to the cif_cod.dic dictionary so that COD entries can be validated.	2008177.cif
858	2009-11-18	cod/cif/ Changing all _chemical_formula_sum values, were necessary, to conform IUCr recommended syntax and sorting order. After this operation, it will be easier to search for structures using the _chemical_formula_sum values. Only those files and thos lines that really needed to be changed were changed; otehrwise the CIFs were not reformatted. The procedure was as follows: first, all files were passed through a 'cif_filter --parse-formula-sum' command, and the lines containing _cif_formula_sum matching tags were extracted. The extracted tags were "spliced" into the CIF files using the ./bin/{un,}grepciftag commands and awk to filter out old tags and add new tags in their place; the replacement was only done if the new tags contained "_cod_" tags ('grep -q _cod_ tmp-$$'), indicating that cif_filter has altered the formula, or the original file did not contain the _chemical_formula_sum tag ('! grep -q _chemical_formula_sum X'), indicating that cif_filter has guessed the chemical_formula_sum from the file (which should not have happened, actually). If the file was different, disregarding spaces, from the original one ('if ! diff -wb X tmp2-$$'), the original was replaced by the new file, to be committed to the repository. The full command for this step was: ( \ set -x; \ find ? -name \.cif \ \| xargs -n1 -iX \ sh -c 'cif_filter --parse-formula-sum X \ \| ./bin/grepciftag _chemical_formula_sum > tmp-$$; \ if grep -q _cod_ tmp-$$ \|\| ! grep -q _chemical_formula_sum X; \ then \ awk "/^#/,/_chemical_formula_sum/{print} /_chemical_formula_sum/{exit}" X \ \| ./bin/ungrepciftag _chemical_formula_sum > tmp2-$$; \ cat tmp-$$ >> tmp2-$$; \ awk "/_chemical_formula_sum/,/\$eof/" X \ \| ./bin/ungrepciftag _chemical_formula_sum >> tmp2-$$; \ if ! diff -wb X tmp2-$$; \ then \ mv -fv tmp2-$$ X; \ fi; \ fi; \ rm -f tmp-$$ tmp2-$$' \ ) >& sort-chemical-formulae-2009.11.16.log Next, the files were searched that differ from their originals only by the order of CIF tags: svn st \ \| awk '/^M/{print $NF}' \ \| sort \| xargs -n1 -iX \ bash -c 'if diff -q <(svn cat X\|sort) <(sort X) >& /dev/null; \ then echo X; \ fi' \ >& only-reordered.lst These files, after manual inspection ('cat only-reordered.lst \| xargs svn diff \| less'), were reverted to the originals: cat only-reordered.lst \| xargs svn revert Finally, a syntax check was performed using 'vcif': svn st \| awk '/^M/{print $NF}' \ \| sort \| xargs -n1 -iX \ sh -c 'echo -n X"\r"; vcif -l 2048 X \|\| { echo == X == ; echo X >&2; }' \ 2> vcif-check-2009.11.18.err A check on the whole COD archive showed the same files as recorded in vcif-check-2009.11.18.err: find ? -name \.cif \ \| sort \ \| xargs -n1 -iX \ sh -c 'echo -n X"\r"; \ vcif -l 2048 X \|\| { echo == X == ; echo X >&2; }' \ 2> vcif-all-check-`-date`.err diff vcif-check-2009.11.18.err vcif-all-check-2009.11.18.err Since no differences were detected in between vcif-check-2009.11.18.err and vcif-all-check-2009.11.18.err, the latter was deleted and is not committed. The check reveled two broken files, 2/2000267.cif and 2/2001000.cif; these were corrected manually. Afther this, one more 'vcif' check showed no syntax errors, and the changes are committed into the COD repository. 19798 files have modifications in this commit, according to svn st \| grep '^M' \| wc -l	2008177.cif
853	2009-11-16	cif/ Reconstructing spacegroup designators from the symmetry operators were possible. The comands used can be found in the log file reformat-spacegroups-2009.11.14.log committed with the current revision. Only lines that contained spacegroup designators were changed, and all files pass vcif test after the conversion.	2008177.cif
481	2008-11-20	Changing volume number in numerous Acta Cryst. C published CIFs from 'C[0-9]?[0-9]' into '[0-9]?[0-9]'. This makes the COD CIF collection more uniform, and also helps the deposition scripts to spot potential duplicates more accurately. The command for this transformation was: for i in 2/.cif; \ do ( \ if grep -q '_journal_volume C' $i && \ grep -q '_journal_name_full .Acta Cryst' $i; \ then \ echo === $i ===; \ perl -i -pe 's/_journal_volume C/_journal_volume /' $i; \ perl -i -pe \ "s/_journal_name_full ./_journal_name_full 'Acta Crystallographica Section C'/" $i ; \ fi \ ) done	2008177.cif
19	2008-01-26	Changing all end-of-line codes from DOS style to UNIX style in all COD CIF files, for more convenient processing: In the cod/cif/ directory: ff \*.cif \| xargs perl -i -pe 's/\r\n/\n/'	2008177.cif
14	2008-01-14	Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files.	2008177.cif
13	2008-01-13	Setting the svn:keywords property to "Author Date Revision URL Id" for all CIF files in the cod/cif directory.	2008177.cif
1	2007-11-30	Adding all .cif files from the COD, downloaded in a Cod.zip file on 2007.02.07 (and the same Cod.zip is downloadable today, on 2007.11.29)	2008177.cif