Crystallography Open Database
- COD Home
- Accessing COD Data
- Add Your Data
- Documentation
Information card for entry 2003685
Preview
| Coordinates | 2003685.cif |
|---|---|
| Original paper (by DOI) | HTML |
| Chemical name | 6-(3,5-Di-O-acetyl-β-D-2-deoxyribofuranosyl)-3,4-dihydro-8-H-pyrimido[4,5-c][1,2]oxazin-7-one |
|---|---|
| Formula | C15 H19 N3 O7 |
| Calculated formula | C15 H19 N3 O7 |
| Title of publication | 6-(3,5-Di-O-acetyl-β-D-2-deoxyribofuranosyl)-3,4-dihydro-8-H-pyrimido[4,5-c][1,2]oxazin-7-one |
| Authors of publication | Van Meervelt, Luc; Kong Thoo Lin, Paul; Brown, Daniel M. |
| Journal of publication | Acta Crystallographica Section C |
| Year of publication | 1995 |
| Journal volume | 51 |
| Journal issue | 7 |
| Pages of publication | 1347 - 1350 |
| a | 14.662 ± 0.003 Å |
| b | 5.419 ± 0.001 Å |
| c | 21.475 ± 0.004 Å |
| α | 90° |
| β | 101.66 ± 0.03° |
| γ | 90° |
| Cell volume | 1671.1 ± 0.6 Å3 |
| Cell temperature | 289 ± 2 K |
| Ambient diffraction temperature | 289 ± 2 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 | 0.1235 |
| Residual factor for significantly intense reflections | 0.0692 |
| Weighted residual factors for all reflections | 0.1726 |
| Weighted residual factors for significantly intense reflections | 0.1468 |
| Goodness-of-fit parameter for all reflections | 1.073 |
| Goodness-of-fit parameter for significantly intense reflections | 1.313 |
| Diffraction radiation wavelength | 1.54184 Å |
| Diffraction radiation type | CuKα |
| Has coordinates | Yes |
| Has disorder | Yes |
| Has Fobs | No |
| Revision | Date | Message | Files |
|---|---|---|---|
| 176428 (current) | 2016-02-13 | Replaced deprecated COD CIF data names with their more modern alternatives. The _cod_cif_authors_sg_Hall and _cod_cif_authors_sg_H-M data items were renamed to _cod_original_sg_symbol_Hall and _cod_cif_authors_sg_H-M respectively. |
2003685.cif |
| 175020 | 2016-01-25 | cif/2/00/ (antanas@echidna.ibt.lt) Adding additional information from the original publication to entry 2003685. |
2003685.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. |
2003685.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" |
2003685.cif |
| 26848 | 2011-09-28 | cif/2/, hkl/2/, html/ Reorganising CIFs of the range 2* into the "prefix-directory" tree. |
2003685.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. |
2003685.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. |
2003685.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 $NF}' \ | xargs -n1 -iI \ bash -c ' \ echo -en I "\r"; \ diff \ <(cif_filter I >& /dev/null) \ <(cif_filter I | cif_filter >& /dev/null) \ || echo "!!! I !!!\n"' This last test discovered one misspelled '_journal_yrae' tag in the 2/2003193.cif entry that was fixed by hand. |
2003685.cif |
| 287 | 2008-03-17 | 20 CIFs fixed |
2003685.cif |
| 20 | 2008-01-26 | Removing white space at the end of all lines from all COD CIF files: in the cod/cif/ directory: ff \*.cif | xargs perl -i -pe 's/\s+\n$/\n/' |
2003685.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/' |
2003685.cif |
| 14 | 2008-01-14 | Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files. |
2003685.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. |
2003685.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) |
2003685.cif |
All data in the COD and the database itself are dedicated to the
public domain and licensed under the
CC0
License
.
Users of the data should acknowledge the original authors of the
structural data.