-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Masaki UNNO, esds (estimated standard deviations) are calculated by full-matrix least-squares refinement as we carried out in order to estimate the uncertaintiy of the occupancy values of the ions in potassium channels. It is described in the Supplemental Material of http://www.sciencemag.org/content/346/6207/352 SHELXL will also provide you with the correlation coefficient between the B-values and the occupancy. If you refine the atom in question anisotropically, the CC drops a little bit. Wit dynamic memory allocation the only limit to full-matrix least-squares refinement is the RAM of your computer (and patience as it may take some time even with only a single refinement cycle). It has been done a 1A resolution (PDB ID 4KGD). Best, Tim On 02/11/2015 09:36 AM, Masaki UNNO wrote:
Hello
We determined the structure of an enzyme-substrate complex. The substrate of the enzyme contains some partially occupied atoms. We were able to calculate the occupancies of these atoms using PHENIX_refine.
By the way, I would like to know the uncertainties of the occupancies of these atoms. How can I estimate the uncertainties? For example, the occupancy of an atom was calculated as 0.65; can we write it as 0.65 (+/- 0.05) or 0.65 (+/- 0.1)? I know that it is related to B-factor and depends on the resolution (number of diffraction data per parameters), but I would like to know how to estimate (calculate?) the uncertainty. Could someone tell me about this issue?
Best regards
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Masaki UNNO
Graduate School of Science and Engineering
Ibaraki University, JAPAN
4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan
Tel&Fax +81-294-38-5041
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- -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) iD8DBQFU2xjdUxlJ7aRr7hoRApLwAJ0UpUbogEfr9SZkkKQ7JDivx13TYwCdFBmw otrEdjnBK+Tit0ze9lzhgXQ= =bp1n -----END PGP SIGNATURE-----