Crystallography Open Database

Information card for entry 4101247

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Coordinates	4101247.cif
Original paper (by DOI)	HTML

Structure parameters

Formula	C846 H2027 B N262 O581 S9.5
Calculated formula	C866.99 H1367.07 N265.96 O639.78 S11.32
Title of publication	Subangstrom crystallography reveals that short ionic hydrogen bonds, and not a His-Asp low-barrier hydrogen bond, stabilize the transition state in serine protease catalysis.
Authors of publication	Fuhrmann, Cynthia N; Daugherty, Matthew D; Agard, David A
Journal of publication	Journal of the American Chemical Society
Year of publication	2006
Journal volume	128
Journal issue	28
Pages of publication	9086 - 9102
a	65.77 ± 0.07 Å
b	65.77 ± 0.07 Å
c	79.55 ± 0.08 Å
α	90°
β	90°
γ	120°
Cell volume	298004 ± 518 Å³
Cell temperature	98 ± 2 K
Ambient diffraction temperature	98 ± 2 K
Number of distinct elements	6
Space group number	154
Hermann-Mauguin space group symbol	P 32 2 1
Hall space group symbol	P 32 2"
Residual factor for all reflections	0.0819
Residual factor for significantly intense reflections	0.0733
Weighted residual factors for significantly intense reflections	0.2061
Weighted residual factors for all reflections included in the refinement	0.2203
Goodness-of-fit parameter for all reflections included in the refinement	1.086
Diffraction radiation wavelength	0.75 Å
Has coordinates	Yes
Has disorder	Yes
Has F_obs	No

Version history

Revision	Date	Message	Files
176467 (current)	2016-02-16	cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in range 4.	4101247.cif
120076	2014-07-11	Adding DOIs to range 4/10 structures.	4101247.cif
34330	2012-02-24	cif/4/ Reorganising CIF range 4 into a prefix tree.	4101247.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.	4101247.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	4101247.cif
396	2008-06-20	Adding new CIF files from J-Am-Chem-Soc-2006/.	4101247.cif