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Information card for entry 2003072
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| Coordinates | 2003072.cif |
|---|---|
| Original IUCr paper | HTML |
| Common name | geraniin |
|---|---|
| Formula | C41 H42 O34 |
| Calculated formula | C41 H42 O34 |
| SMILES | [C@H]1(OC(=O)c2cc(O)c(O)c(O)c2)[C@@H]2OC(=O)c3cc(O)c(O)c4O[C@]5(C(=O)C=C(C(=O)O[C@H]6[C@@H]2OC(=O)c2cc(O)c(O)c(O)c2c2c(C(=O)OC[C@H]6O1)cc(O)c(O)c2O)[C@@H](c34)C5(O)O)O.O.O.O.O.O.O.O |
| Title of publication | Structure of the Tannin Geraniin Based on Conventional X-ray Data at 295 K and on Synchrotron Data at 293 and 120 K |
| Authors of publication | Luger, Peter; Weber, Manuela; Kashino,Setsuo; Amakura, Yoshiaki; Yoshida, Takashi; Okuda, Takuo; Beurskens, Gezina; Dauter, Zbigniew |
| Journal of publication | Acta Crystallographica Section B |
| Year of publication | 1998 |
| Journal volume | 54 |
| Journal issue | 5 |
| Pages of publication | 687 - 694 |
| a | 13 ± 0.004 Å |
| b | 29.1 ± 0.004 Å |
| c | 11.6 ± 0.004 Å |
| α | 90° |
| β | 90° |
| γ | 90° |
| Cell volume | 4388 ± 2 Å3 |
| Cell temperature | 293 ± 2 K |
| Ambient diffraction temperature | 293 ± 2 K |
| Number of distinct elements | 3 |
| Space group number | 19 |
| Hermann-Mauguin space group symbol | P 21 21 21 |
| Hall space group symbol | P 2ac 2ab |
| Residual factor for all reflections | 0.0614 |
| Residual factor for significantly intense reflections | 0.0557 |
| Weighted residual factors for all reflections | 0.1599 |
| Weighted residual factors for significantly intense reflections | 0.1535 |
| Goodness-of-fit parameter for all reflections | 1.046 |
| Goodness-of-fit parameter for significantly intense reflections | 1.074 |
| Diffraction radiation wavelength | 0.86 Å |
| Diffraction radiation type | synchrotron |
| Has coordinates | Yes |
| Has disorder | No |
| Has Fobs | No |
| Revision | Date | Message | Files |
|---|---|---|---|
| 288306 (current) | 2023-12-14 | cif/2/00/30/ Corrected the ATOM_TYPE loop in entries 2003072, 2003073 by removing extra data values which were incorrectly copied from other data items (e.g. 'Imaging Plate', 'SHELXL-93 (Sheldrick, 1993)'). |
2003072.cif |
| 176759 | 2016-02-19 | cif/2/ (antanas@echidna.ibt.lt) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in subrange 2/00. |
2003072.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. |
2003072.cif |
| 129439 | 2015-01-07 | cod/ (robertas@burundukas) Correcting values of _exptl_crystal_density_meas and _exptl_crystal_density_method data items: codsql "select codid from validation where message like '%\\'_exptl_crystal_density_meas\\' value \"not measured\" is %'" -NB \ | codid2file \ | xargs perl -i -pe "s/_exptl_crystal_density_meas\\s+'not +measured'/_exptl_crystal_density_meas ?/i; \ s/_exptl_crystal_density_method\\s+('not +measured'|\\?|none)/_exptl_crystal_density_method ./i" |
2003072.cif |
| 91933 | 2013-12-28 | cif/ (saulius@koala.ibt.lt) Adding DOIs that could be assigned unambiguously to the range 2x CIFs. |
2003072.cif |
| 32112 | 2012-02-03 | cif/: committing an update of 45+ thous files, with information appended from the originals. | 2003072.cif |
| 26848 | 2011-09-28 | cif/2/, hkl/2/, html/ Reorganising CIFs of the range 2* into the "prefix-directory" tree. |
2003072.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). |
2003072.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. |
2003072.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. |
2003072.cif |
| 846 | 2009-11-14 | cif/ Fixing _journal_volume values that had series letters prepended to them. Now the series letters are appended to the _journal_name_full, if needed, and the _journal_volume is purely numeric. To mimimise textual changes to CIFs this was done in several stages. First of all, a list of _journal_volume was compiled from the COD CIF collection: bash -xc 'find ? -name \*.cif \ | xargs cif_values \ --file \ --tag _journal_volume' \ >& cod-journal-volumes-`-date`.log & giving us a cod-journal-volumes-2009.11.13.log file (committed for reference as well). Then a list of volume names with letters was extracted and most of them transformed automatically into a correct form: awk '$3~/^[A-Z][0-9]/' cod-journal-volumes-2009.11.13.log \ | awk '{print $1}' \ | xargs -n1 -iI \ bash -c 'echo === I ===;\ awk "/^#/,/^data_/{print}/^data_/{exit}" I > tmp-$$; \ cif_adjust_journal_name_volume I \ | grep -E "_journal_name_full|_journal_volume" >> tmp-$$; \ awk "/^data_/,/\$eof/" I \ | grep -vE "^(data_|_journal_name_full|_journal_volume)" >> tmp-$$;\ mv -v tmp-$$ I' Note that this procedure assumes that all tags are at the beginning of the line, each value follows its tag on the same line, and there is only one tag per line. This procedure is not suitable for general CIFs, but fortunately, only very few CIFs in COD do not conform these rules. After the automatic conversion, a syntax check was run: svn st ? \ | awk '{print $NF}' \ | xargs -n1 -iI sh -c 'echo -n I"\r"; vcif -l 2048 I || echo "!!! I !!!\n"' Entries that were found to have errors (very few, less than 10) were reverted and fixed manually. The entries that had letters embedded into them were grepped separately: awk '$3~/[A-Z][0-9]/' cod-journal-volumes-2009.11.13.log \ | awk '$3~/^[^A-Z]/' and fixed manually. After all fixes, the previous 'vcif' test was rerun, yielding no syntax errors, and in addition a 'cif_filter' roundtrip test was run: svn st ? \ | awk '{print $NF}' \ | xargs -n1 -iI \ bash -c ' \ echo -en I "\r"; \ diff \ <(cif_filter I >& /dev/null) \ <(cif_filter I | cif_filter >& /dev/null) \ || echo "!!! I !!!\n"' This last test discovered one misspelled '_journal_yrae' tag in the 2/2003193.cif entry that was fixed by hand. |
2003072.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/' |
2003072.cif |
| 14 | 2008-01-14 | Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files. |
2003072.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. |
2003072.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) |
2003072.cif |
All data in the COD and the database itself are dedicated to the
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Users of the data should acknowledge the original authors of the
structural data.