Crystallography Open Database

Information card for entry 2006667

2006666 << 2006667 >> 2006668

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Coordinates	2006667.cif
Original IUCr paper	HTML
External links	ChemSpider

Structure parameters

Common name	Pseudouridine
Chemical name	2,4(1H,3H)-Pyrimidinedione,5-β-D-ribofuranosyl
Formula	C9 H12 N2 O6
Calculated formula	C9 H12 N2 O6
SMILES	N1C(=O)NC(=O)C(=C1)[C@@H]1O[C@@H]([C@H]([C@H]1O)O)CO
Title of publication	Pseudouridine
Authors of publication	Hempel, Andrew; Lane, Byron G.; Camerman, Norman
Journal of publication	Acta Crystallographica Section C
Year of publication	1997
Journal volume	53
Journal issue	11
Pages of publication	1707 - 1709
a	5.1318 ± 0.0002 Å
b	6.9156 ± 0.0003 Å
c	14.9166 ± 0.0006 Å
α	83.3087 ± 0.0014°
β	88.388 ± 0.002°
γ	71.835 ± 0.002°
Cell volume	499.55 ± 0.04 Å³
Cell temperature	293 ± 2 K
Ambient diffraction temperature	293 ± 2 K
Number of distinct elements	4
Space group number	1
Hermann-Mauguin space group symbol	P 1
Hall space group symbol	P 1
Residual factor for all reflections	0.2477
Residual factor for significantly intense reflections	0.0918
Weighted residual factors for all reflections	0.2851
Weighted residual factors for significantly intense reflections	0.1898
Goodness-of-fit parameter for all reflections	0.927
Goodness-of-fit parameter for significantly intense reflections	1.044
Diffraction radiation wavelength	0.71013 Å
Diffraction radiation type	MoKα
Has coordinates	Yes
Has disorder	No
Has F_obs	No

Version history

Revision	Date	Message	Files
201955 (current)	2017-10-13	cif/2/ Marking COD entries in range 2/00 that are known to be related to ChemSpider entries using the _cod_related_entry data loop.	2006667.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.	2006667.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.	2006667.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 {}'	2006667.cif
91933	2013-12-28	cif/ (saulius@koala.ibt.lt) Adding DOIs that could be assigned unambiguously to the range 2x CIFs.	2006667.cif
32112	2012-02-03	cif/: committing an update of 45+ thous files, with information appended from the originals.	2006667.cif
26848	2011-09-28	cif/2/, hkl/2/, html/ Reorganising CIFs of the range 2* into the "prefix-directory" tree.	2006667.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).	2006667.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.	2006667.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.	2006667.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.	2006667.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	2006667.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/'	2006667.cif
14	2008-01-14	Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files.	2006667.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.	2006667.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)	2006667.cif