CC1/2 - Revision history

Kay at 09:32, 31 March 2018

2018-03-31T09:32:49Z

← Older revision		Revision as of 11:32, 31 March 2018
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	Examples for citations from papers using (possibly among other criteria) CC<sub>1/2</sub> and/or the paired refinement method (~~first~~ reference below) for finding the high-resolution cutoff.		Examples for citations from papers using (possibly among other criteria) CC<sub>1/2</sub> and/or the paired refinement method (reference 1, below) for finding the high-resolution cutoff.

	# "In choosing our highest-resolution cutoff we chose shells, which still fulfil CC1/2 (ref. 57) >25% and I/σ(I) greater than or equal to 0.5 and which were supported by our results from the paired refinement method (ref. 57). Choosing a lower resolution cutoff did not improve the overall quality of the maps." Models were refined at 6.0 and 3.4 Å, respectively [http://www.nature.com/ncomms/2016/160419/ncomms11184/full/ncomms11184.html].		# "In choosing our highest-resolution cutoff we chose shells, which still fulfil CC1/2 (ref. 57) >25% and I/σ(I) greater than or equal to 0.5 and which were supported by our results from the paired refinement method (ref. 57). Choosing a lower resolution cutoff did not improve the overall quality of the maps." Models were refined at 6.0 and 3.4 Å, respectively http://www.nature.com/ncomms/2016/160419/ncomms11184/full/ncomms11184.html.
	# http://www.nature.com/nature/journal/vaop/ncurrent/full/nature18934.html#methods "The final data set used for structure solution and refinement was merged from data from nine crystals for apo-SMOΔC and two crystals for vismo-SMOΔC. Data collection statistics are shown in Extended Data Table 1." That table shows high resolution values of 3.2 and 3.3 Å, respectively, with CC<sub>1/2</sub> of 0.237 and 0.357, and I/σ(I) of 0.6. It also gives CC, CC<sub>work</sub> and CC<sub>free</sub> and demonstrates that CC<sub>work</sub> < CC, as is to be expected.		# http://www.nature.com/nature/journal/vaop/ncurrent/full/nature18934.html#methods "The final data set used for structure solution and refinement was merged from data from nine crystals for apo-SMOΔC and two crystals for vismo-SMOΔC. Data collection statistics are shown in Extended Data Table 1." That table shows high resolution values of 3.2 and 3.3 Å, respectively, with CC<sub>1/2</sub> of 0.237 and 0.357, and I/σ(I) of 0.6. It also gives CC, CC<sub>work</sub> and CC<sub>free</sub> and demonstrates that CC<sub>work</sub> < CC, as is to be expected.
	# http://www.nature.com/nature/journal/vaop/ncurrent/full/nature19825.html This describes the results of an experimental phasing for XFEL data. The authors had the insight: "Handling of negative intensities was then implemented in cctbx.xfel, allowing the production of meliorated post-refined data sets with intensity distributions that no longer have abnormal reflection intensity metrics (L-test and NZ-test). We used the same criteria for the resolution cut-off, based on completeness on (>90%), redundancy (>4) and CC<sub>1/2</sub> (>0.14); in all data sets, the resulting I/sigI in the highest resolution shells was greater than 0.5. While inclusion of negative intensities dramatically affects I/sigI, it results in stabilization of the refinement for the three native structures (pH 5, pH 7 and pH 10), requiring us to impose a lower weight on geometry in phenix.refine to obtain a structure with a plateauing Rfree. Inclusion of negative intensities in the data sets also resulted in a decrease of noise levels in q-weighted structure factor amplitude Fourier difference maps (see below). At the atomic level, the only noticeable change between structures refined with and without negative intensities included is an increase in the B-factors, reflecting the increase of the Wilson-B—and possibly giving a more realistic description of the BinAB structures at room temperature." Their findings seem to nicely support reference 2 (below).		# http://www.nature.com/nature/journal/vaop/ncurrent/full/nature19825.html This describes the results of an experimental phasing for XFEL data. The authors had the insight: "Handling of negative intensities was then implemented in cctbx.xfel, allowing the production of meliorated post-refined data sets with intensity distributions that no longer have abnormal reflection intensity metrics (L-test and NZ-test). We used the same criteria for the resolution cut-off, based on completeness on (>90%), redundancy (>4) and CC<sub>1/2</sub> (>0.14); in all data sets, the resulting I/sigI in the highest resolution shells was greater than 0.5. While inclusion of negative intensities dramatically affects I/sigI, it results in stabilization of the refinement for the three native structures (pH 5, pH 7 and pH 10), requiring us to impose a lower weight on geometry in phenix.refine to obtain a structure with a plateauing Rfree. Inclusion of negative intensities in the data sets also resulted in a decrease of noise levels in q-weighted structure factor amplitude Fourier difference maps (see below). At the atomic level, the only noticeable change between structures refined with and without negative intensities included is an increase in the B-factors, reflecting the increase of the Wilson-B—and possibly giving a more realistic description of the BinAB structures at room temperature." Their findings seem to nicely support reference 2 (below).

Kay at 19:21, 28 September 2016

2016-09-28T19:21:27Z

← Older revision		Revision as of 21:21, 28 September 2016
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	Examples for citations from papers using (possibly among other criteria) CC<sub>1/2</sub> and/or the paired refinement method (reference below) for finding the high-resolution cutoff.		Examples for citations from papers using (possibly among other criteria) CC<sub>1/2</sub> and/or the paired refinement method (first reference below) for finding the high-resolution cutoff.

	# "In choosing our highest-resolution cutoff we chose shells, which still fulfil CC1/2 (ref. 57) >25% and I/σ(I) greater than or equal to 0.5 and which were supported by our results from the paired refinement method (ref. 57). Choosing a lower resolution cutoff did not improve the overall quality of the maps." Models were refined at 6.0 and 3.4 Å, respectively [http://www.nature.com/ncomms/2016/160419/ncomms11184/full/ncomms11184.html].		# "In choosing our highest-resolution cutoff we chose shells, which still fulfil CC1/2 (ref. 57) >25% and I/σ(I) greater than or equal to 0.5 and which were supported by our results from the paired refinement method (ref. 57). Choosing a lower resolution cutoff did not improve the overall quality of the maps." Models were refined at 6.0 and 3.4 Å, respectively [http://www.nature.com/ncomms/2016/160419/ncomms11184/full/ncomms11184.html].
	# http://www.nature.com/nature/journal/vaop/ncurrent/full/nature18934.html#methods "The final data set used for structure solution and refinement was merged from data from nine crystals for apo-SMOΔC and two crystals for vismo-SMOΔC. Data collection statistics are shown in Extended Data Table 1." That table shows high resolution values of 3.2 and 3.3 Å, respectively, with CC<sub>1/2</sub> of 0.237 and 0.357, and I/σ(I) of 0.6. It also gives CC, CC<sub>work</sub> and CC<sub>free</sub> and demonstrates that CC<sub>work</sub> < CC, as is to be expected.		# http://www.nature.com/nature/journal/vaop/ncurrent/full/nature18934.html#methods "The final data set used for structure solution and refinement was merged from data from nine crystals for apo-SMOΔC and two crystals for vismo-SMOΔC. Data collection statistics are shown in Extended Data Table 1." That table shows high resolution values of 3.2 and 3.3 Å, respectively, with CC<sub>1/2</sub> of 0.237 and 0.357, and I/σ(I) of 0.6. It also gives CC, CC<sub>work</sub> and CC<sub>free</sub> and demonstrates that CC<sub>work</sub> < CC, as is to be expected.
			# http://www.nature.com/nature/journal/vaop/ncurrent/full/nature19825.html This describes the results of an experimental phasing for XFEL data. The authors had the insight: "Handling of negative intensities was then implemented in cctbx.xfel, allowing the production of meliorated post-refined data sets with intensity distributions that no longer have abnormal reflection intensity metrics (L-test and NZ-test). We used the same criteria for the resolution cut-off, based on completeness on (>90%), redundancy (>4) and CC<sub>1/2</sub> (>0.14); in all data sets, the resulting I/sigI in the highest resolution shells was greater than 0.5. While inclusion of negative intensities dramatically affects I/sigI, it results in stabilization of the refinement for the three native structures (pH 5, pH 7 and pH 10), requiring us to impose a lower weight on geometry in phenix.refine to obtain a structure with a plateauing Rfree. Inclusion of negative intensities in the data sets also resulted in a decrease of noise levels in q-weighted structure factor amplitude Fourier difference maps (see below). At the atomic level, the only noticeable change between structures refined with and without negative intensities included is an increase in the B-factors, reflecting the increase of the Wilson-B—and possibly giving a more realistic description of the BinAB structures at room temperature." Their findings seem to nicely support reference 2 (below).

	== References ==		== References ==

			# [http://science.sciencemag.org/content/336/6084/1030.full P.A. Karplus and K. Diederichs (2012) Linking Crystallographic Model and Data Quality. Science ''336'', 1030-1033]
	[http://science.sciencemag.org/content/336/6084/1030.full P.A. Karplus and K. Diederichs (2012) Linking Crystallographic Model and Data Quality. Science ''336'', 1030-1033]		# [https://cms.uni-konstanz.de/index.php?eID=tx_nawsecuredl&u=0&g=0&t=1475180069&hash=f8c4218fb99e95d6a065df88f0de9340421fa902&file=fileadmin/biologie/ag-strucbio/pdfs/Diederichs2013_ActaCrystD.pdf Diederichs, K., Karplus PA. (2013) Better models by discarding data? Acta Cryst. D69, 1215-1222.]

Kay at 10:01, 26 July 2016

2016-07-26T10:01:31Z

← Older revision		Revision as of 12:01, 26 July 2016
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	Examples for citations from papers using (possibly among other criteria) CC<sub>1/2</sub> and/or the paired refinement method (reference below) for finding the high-resolution cutoff.		Examples for citations from papers using (possibly among other criteria) CC<sub>1/2</sub> and/or the paired refinement method (reference below) for finding the high-resolution cutoff.

	# "In choosing our highest-resolution cutoff we chose shells, which still fulfil CC1/2 (ref. 57) >25% and I/σ(I)greater than or equal to 0.5 and which were supported by our results from the paired refinement method (ref. 57). Choosing a lower resolution cutoff did not improve the overall quality of the maps." Models were refined at 6.0 and 3.4 Å, respectively [http://www.nature.com/ncomms/2016/160419/ncomms11184/full/ncomms11184.html].		# "In choosing our highest-resolution cutoff we chose shells, which still fulfil CC1/2 (ref. 57) >25% and I/σ(I) greater than or equal to 0.5 and which were supported by our results from the paired refinement method (ref. 57). Choosing a lower resolution cutoff did not improve the overall quality of the maps." Models were refined at 6.0 and 3.4 Å, respectively [http://www.nature.com/ncomms/2016/160419/ncomms11184/full/ncomms11184.html].
			# http://www.nature.com/nature/journal/vaop/ncurrent/full/nature18934.html#methods "The final data set used for structure solution and refinement was merged from data from nine crystals for apo-SMOΔC and two crystals for vismo-SMOΔC. Data collection statistics are shown in Extended Data Table 1." That table shows high resolution values of 3.2 and 3.3 Å, respectively, with CC<sub>1/2</sub> of 0.237 and 0.357, and I/σ(I) of 0.6. It also gives CC, CC<sub>work</sub> and CC<sub>free</sub> and demonstrates that CC<sub>work</sub> < CC, as is to be expected.

Kay: /* References */

2016-04-23T07:28:20Z

References

← Older revision		Revision as of 09:28, 23 April 2016
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	P.A. Karplus and K. Diederichs (2012) Linking Crystallographic Model and Data Quality. Science ''336'', 1030-1033		[http://science.sciencemag.org/content/336/6084/1030.full P.A. Karplus and K. Diederichs (2012) Linking Crystallographic Model and Data Quality. Science ''336'', 1030-1033]

Kay: Created page with "Examples for citations from papers using (possibly among other criteria) CC_1/2 and/or the paired refinement method (reference below) for finding the high-resolution..."

2016-04-23T07:27:11Z

Created page with "Examples for citations from papers using (possibly among other criteria) CC<sub>1/2</sub> and/or the paired refinement method (reference below) for finding the high-resolution..."

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Examples for citations from papers using (possibly among other criteria) CC<sub>1/2</sub> and/or the paired refinement method (reference below) for finding the high-resolution cutoff.

# "In choosing our highest-resolution cutoff we chose shells, which still fulfil CC1/2 (ref. 57) >25% and I/σ(I)greater than or equal to 0.5 and which were supported by our results from the paired refinement method (ref. 57). Choosing a lower resolution cutoff did not improve the overall quality of the maps." Models were refined at 6.0 and 3.4 Å, respectively [http://www.nature.com/ncomms/2016/160419/ncomms11184/full/ncomms11184.html].

== References ==

P.A. Karplus and K. Diederichs (2012) Linking Crystallographic Model and Data Quality. Science ''336'', 1030-1033

CC1/2 - Revision history

Kay at 09:32, 31 March 2018

Kay at 19:21, 28 September 2016

Kay at 10:01, 26 July 2016

Kay: /* References */

Kay: Created page with "Examples for citations from papers using (possibly among other criteria) CC1/2 and/or the paired refinement method (reference below) for finding the high-resolution..."

Kay: Created page with "Examples for citations from papers using (possibly among other criteria) CC_1/2 and/or the paired refinement method (reference below) for finding the high-resolution..."