Crystallography Open Database

Information card for entry 2219561

2219560 << 2219561 >> 2219562

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Coordinates	2219561.cif
Structure factors	2219561.hkl
Original IUCr paper	HTML

Structure parameters

Common name	1S,2S-1-((pyridin-3'-yl)methyl)pyrrolidine-2-carboxylic acid-1, 1'-ium dichloride semihydrate
Chemical name	(1<i>S</i>,2<i>S</i>)-2-Carboxy-1-(3-pyridiniomethyl)pyrrolidin-1-ium dichloride hemihydrate
Formula	C11 H17 Cl2 N2 O2.5
Calculated formula	C11 H17 Cl2 N2 O2.5
Title of publication	(1<i>S</i>,2<i>S</i>)-2-Carboxy-1-(3-pyridiniomethyl)pyrrolidin-1-ium dichloride hemihydrate
Authors of publication	Dai, Jing; Wen, Xiao-Chun
Journal of publication	Acta Crystallographica Section E
Year of publication	2008
Journal volume	64
Journal issue	10
Pages of publication	o1960
a	13.07 ± 0.005 Å
b	6.9215 ± 0.0015 Å
c	15.027 ± 0.005 Å
α	90°
β	97.9 ± 0.02°
γ	90°
Cell volume	1346.5 ± 0.7 Å³
Cell temperature	298 ± 2 K
Ambient diffraction temperature	298 ± 2 K
Number of distinct elements	5
Space group number	5
Hermann-Mauguin space group symbol	C 1 2 1
Hall space group symbol	C 2y
Residual factor for all reflections	0.0366
Residual factor for significantly intense reflections	0.033
Weighted residual factors for significantly intense reflections	0.0824
Weighted residual factors for all reflections included in the refinement	0.0854
Goodness-of-fit parameter for all reflections included in the refinement	1.073
Diffraction radiation wavelength	0.71073 Å
Diffraction radiation type	MoKα
Has coordinates	Yes
Has disorder	Yes
Has F_obs	Yes

Version history

Revision	Date	Message	Files
181115 (current)	2016-04-03	hkl/2/21/ (antanas@echidna) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in subrange 2/21/95.	2219561.cif 2219561.hkl
176435	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.	2219561.cif 2219561.hkl
91933	2013-12-28	cif/ (saulius@koala.ibt.lt) Adding DOIs that could be assigned unambiguously to the range 2x CIFs.	2219561.cif 2219561.hkl
88064	2013-08-29	Adding _cod_database_fobs_code data item to all COD CIFs that have Fobs deposited and did not have this data item yet.	2219561.cif 2219561.hkl
32112	2012-02-03	cif/: committing an update of 45+ thous files, with information appended from the originals.	2219561.cif 2219561.hkl
26848	2011-09-28	cif/2/, hkl/2/, html/ Reorganising CIFs of the range 2* into the "prefix-directory" tree.	2219561.cif 2219561.hkl
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).	2219561.cif 2219561.hkl
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.	2219561.cif 2219561.hkl
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.	2219561.cif 2219561.hkl
903	2009-11-23	cif/ Setting svn:keywords property on those CIFs that did not have them.	2219561.cif 2219561.hkl
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	2219561.cif 2219561.hkl
691	2009-05-03	Depositing the first portion of the Fobs data CIFs. These are CIFs from the Acta Cryst. journals, where the correspondence of the coordinate CIF and the Fobs CIF could be unambiguously determined automatically. In these files, cell constatnts match exctely, being equal with the floating point '==' operator in Perl. For the future depositions, such requirement is too strict, since sometimes cell constants in the coordinate and the Fobs files differ by a rounding error. Thus, a small tollerance will have to be introduced into the COD Fobs deposition scripts.	2219561.cif 2219561.hkl
605	2009-03-27	Adding CIFs from the Acta-Cryst-E-2008_09-12/ deposition.	2219561.cif