Crystallography Open Database

Information card for entry 2206377

2206376 << 2206377 >> 2206378

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Coordinates	2206377.cif
Structure factors	2206377.hkl
Original IUCr paper	HTML
External links	ChemSpider

Structure parameters

Chemical name	(2R,3S,4S,5R)-Methyl 5-cyano-2,3:4,5-di-O-isopropylidene-2,3,4,5- tetrahydroxypentanoate
Formula	C13 H19 N O6
Calculated formula	C13 H19 N O6
SMILES	COC(=O)[C@@H]1OC(C)(C)O[C@H]1[C@@H]1[C@@H](C#N)OC(C)(C)O1
Title of publication	(2<i>R</i>,3<i>S</i>,4<i>S</i>,5<i>R</i>)-Methyl 5-cyano-2,3:4,5-di-<i>O</i>-isopropylidene-2,3,4,5-tetrahydroxypentanoate
Authors of publication	Andreas Glawar; Benjamin A. Mayes; David Watkin; George W. J. Fleet
Journal of publication	Acta Crystallographica Section E
Year of publication	2005
Journal volume	61
Journal issue	8
Pages of publication	o2727 - o2729
a	10.4312 ± 0.0003 Å
b	5.4469 ± 0.0001 Å
c	13.0536 ± 0.0005 Å
α	90°
β	93.4825 ± 0.001°
γ	90°
Cell volume	740.31 ± 0.04 Å³
Cell temperature	190 K
Ambient diffraction temperature	190 K
Number of distinct elements	4
Space group number	4
Hermann-Mauguin space group symbol	P 1 21 1
Hall space group symbol	P 2yb
Residual factor for all reflections	0.0318
Residual factor for significantly intense reflections	0.0318
Weighted residual factors for all reflections	0.0693
Weighted residual factors for significantly intense reflections	0.0693
Weighted residual factors for all reflections included in the refinement	0.0693
Goodness-of-fit parameter for all reflections included in the refinement	0.9885
Diffraction radiation wavelength	0.71073 Å
Diffraction radiation type	MoKα
Has coordinates	Yes
Has disorder	No
Has F_obs	Yes

Version history

Revision	Date	Message	Files
201973 (current)	2017-10-13	cif/2/ Marking COD entries in range 2/20 that are known to be related to ChemSpider entries using the _cod_related_entry data loop.	2206377.cif 2206377.hkl
180983	2016-04-03	hkl/2/20/ (antanas@echidna) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in subrange 2/20/63.	2206377.cif 2206377.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.	2206377.cif 2206377.hkl
91933	2013-12-28	cif/ (saulius@koala.ibt.lt) Adding DOIs that could be assigned unambiguously to the range 2x CIFs.	2206377.cif 2206377.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.	2206377.cif 2206377.hkl
32112	2012-02-03	cif/: committing an update of 45+ thous files, with information appended from the originals.	2206377.cif 2206377.hkl
26848	2011-09-28	cif/2/, hkl/2/, html/ Reorganising CIFs of the range 2* into the "prefix-directory" tree.	2206377.cif 2206377.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).	2206377.cif 2206377.hkl
26025	2011-09-16	hkl/2/ Adding assigned Fobs files for the 1980-2010 IUCr data.	2206377.cif 2206377.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.	2206377.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.	2206377.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	2206377.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.	2206377.cif
326	2008-04-03	Adding all Acta Cryst. B, C, and E missing retrospective CIF files up to 2008 February, generated from the files that were automatically downloaded from the IUCr site.	2206377.cif