3CSL - Revision history

Kay: JOBS=. -> JOB=

2020-05-12T19:42:51Z

JOBS=. -> JOB=

← Older revision		Revision as of 21:42, 12 May 2020
Line 17:		Line 17:

	It turns out that the spot shapes are actually so irregular that XDS stops after the IDXREF step, with a long warning message. This is because it cannot index (within default error margins) enough reflections (50% is the cutoff). When that occurs, one simply continues with the step after IDXREF:		It turns out that the spot shapes are actually so irregular that XDS stops after the IDXREF step, with a long warning message. This is because it cannot index (within default error margins) enough reflections (50% is the cutoff). When that occurs, one simply continues with the step after IDXREF:
	~~JOBS~~= DEFPIX INTEGRATE CORRECT		JOB= DEFPIX INTEGRATE CORRECT

	Other than that, the three MAD wavelengths can be processed once with default parameters, as written into [[XDS.INP]] by [[generate_XDS.INP]]. This data reduction therefore proceeds in spacegroup P1, but the correct spacegroup (22) is identified by CORRECT.		Other than that, the three MAD wavelengths can be processed once with default parameters, as written into [[XDS.INP]] by [[generate_XDS.INP]]. This data reduction therefore proceeds in spacegroup P1, but the correct spacegroup (22) is identified by CORRECT.
Line 24:		Line 24:
	mv GXPAM.XDS XPARM.XDS		mv GXPAM.XDS XPARM.XDS
	and modify XDS.INP to read		and modify XDS.INP to read
	~~JOBS~~= INTEGRATE CORRECT		JOB= INTEGRATE CORRECT
	Afterwards, another xds_par run gives the final intensities. Repeating this optimization sometimes helps.		Afterwards, another xds_par run gives the final intensities. Repeating this optimization sometimes helps.

Karsten at 13:12, 24 March 2020

2020-03-24T13:12:36Z

← Older revision		Revision as of 15:12, 24 March 2020
Line 28:		Line 28:

	=== Peak ===		=== Peak ===
	360 frames (0.5° oscillation) at the peak wavelength were collected after the high-remote data. They can be downloaded from [~~ftp~~://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.9 Gb). This peak dataset is somewhat difficult to index; if the results are really bad (e.g. distance refining far away from 370 mm) with the default 180 frames, then just try with 90 or 270 frames.		360 frames (0.5° oscillation) at the peak wavelength were collected after the high-remote data. They can be downloaded from [https://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.9 Gb). This peak dataset is somewhat difficult to index; if the results are really bad (e.g. distance refining far away from 370 mm) with the default 180 frames, then just try with 90 or 270 frames.

	This is an excerpt from [[CORRECT.LP]] :		This is an excerpt from [[CORRECT.LP]] :
Line 122:		Line 122:
	=== High-remote ===		=== High-remote ===

	Due to a beamline problem, high-remote data collection stopped after 269 frames of 0.5° (the final frame is already affected). After restart of the beamline, another 100 frames were collected but they later turned out to merge badly with the first 269 frames - a hint that the monochromator was still heating up, or similar. So the latter frames were left out. The 269 frames are [~~ftp~~://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.4 Gb; you guessed that the file is called 3csl-hrem.tar, right?).		Due to a beamline problem, high-remote data collection stopped after 269 frames of 0.5° (the final frame is already affected). After restart of the beamline, another 100 frames were collected but they later turned out to merge badly with the first 269 frames - a hint that the monochromator was still heating up, or similar. So the latter frames were left out. The 269 frames are [https://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.4 Gb; you guessed that the file is called 3csl-hrem.tar, right?).

	From CORRECT.LP :		From CORRECT.LP :
Line 157:		Line 157:
	=== Inflection ===		=== Inflection ===

	360 frames (0.5° oscillation) at the inflection wavelength were collected after the peak data. They can be downloaded from [~~ftp~~://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.8 Gb).		360 frames (0.5° oscillation) at the inflection wavelength were collected after the peak data. They can be downloaded from [https://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.8 Gb).

	CORRECT.LP has:		CORRECT.LP has:
Line 321:		Line 321:
	== Availability of data ==		== Availability of data ==

	There are files with amplitudes (3csl-pk-F.mtz, 3csl-rh-F.mtz, 3csl-ip-F.mtz) and intensities (3csl-pk-I.mtz, 3csl-rh-I.mtz, 3csl-ip-I.mtz) as well as mad_i.pdb and mad_i.phs (written by SHELXE) available from [~~ftp~~://{{SERVERNAME}}/pub/xds-datared/3csl/]. Furthermore the raw data can be downloaded there.		There are files with amplitudes (3csl-pk-F.mtz, 3csl-rh-F.mtz, 3csl-ip-F.mtz) and intensities (3csl-pk-I.mtz, 3csl-rh-I.mtz, 3csl-ip-I.mtz) as well as mad_i.pdb and mad_i.phs (written by SHELXE) available from [https://{{SERVERNAME}}/pub/xds-datared/3csl/]. Furthermore the raw data can be downloaded there.

	=== additional information for those who want to complete the structure ===		=== additional information for those who want to complete the structure ===

Karsten at 16:41, 19 December 2019

2019-12-19T16:41:01Z

← Older revision		Revision as of 18:41, 19 December 2019
Line 28:		Line 28:

	=== Peak ===		=== Peak ===
	360 frames (0.5° oscillation) at the peak wavelength were collected after the high-remote data. They can be downloaded from [ftp://~~turn5.biologie.uni-konstanz.de~~/pub/xds-datared/3csl/ here] (1.9 Gb). This peak dataset is somewhat difficult to index; if the results are really bad (e.g. distance refining far away from 370 mm) with the default 180 frames, then just try with 90 or 270 frames.		360 frames (0.5° oscillation) at the peak wavelength were collected after the high-remote data. They can be downloaded from [ftp://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.9 Gb). This peak dataset is somewhat difficult to index; if the results are really bad (e.g. distance refining far away from 370 mm) with the default 180 frames, then just try with 90 or 270 frames.

	This is an excerpt from [[CORRECT.LP]] :		This is an excerpt from [[CORRECT.LP]] :
Line 122:		Line 122:
	=== High-remote ===		=== High-remote ===

	Due to a beamline problem, high-remote data collection stopped after 269 frames of 0.5° (the final frame is already affected). After restart of the beamline, another 100 frames were collected but they later turned out to merge badly with the first 269 frames - a hint that the monochromator was still heating up, or similar. So the latter frames were left out. The 269 frames are [ftp://~~turn5.biologie.uni-konstanz.de~~/pub/xds-datared/3csl/ here] (1.4 Gb; you guessed that the file is called 3csl-hrem.tar, right?).		Due to a beamline problem, high-remote data collection stopped after 269 frames of 0.5° (the final frame is already affected). After restart of the beamline, another 100 frames were collected but they later turned out to merge badly with the first 269 frames - a hint that the monochromator was still heating up, or similar. So the latter frames were left out. The 269 frames are [ftp://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.4 Gb; you guessed that the file is called 3csl-hrem.tar, right?).

	From CORRECT.LP :		From CORRECT.LP :
Line 157:		Line 157:
	=== Inflection ===		=== Inflection ===

	360 frames (0.5° oscillation) at the inflection wavelength were collected after the peak data. They can be downloaded from [ftp://~~turn5.biologie.uni-konstanz.de~~/pub/xds-datared/3csl/ here] (1.8 Gb).		360 frames (0.5° oscillation) at the inflection wavelength were collected after the peak data. They can be downloaded from [ftp://{{SERVERNAME}}/pub/xds-datared/3csl/ here] (1.8 Gb).

	CORRECT.LP has:		CORRECT.LP has:
Line 321:		Line 321:
	== Availability of data ==		== Availability of data ==

	There are files with amplitudes (3csl-pk-F.mtz, 3csl-rh-F.mtz, 3csl-ip-F.mtz) and intensities (3csl-pk-I.mtz, 3csl-rh-I.mtz, 3csl-ip-I.mtz) as well as mad_i.pdb and mad_i.phs (written by SHELXE) available from [ftp://~~turn5.biologie.uni-konstanz.de~~/pub/xds-datared/3csl/]. Furthermore the raw data can be downloaded there.		There are files with amplitudes (3csl-pk-F.mtz, 3csl-rh-F.mtz, 3csl-ip-F.mtz) and intensities (3csl-pk-I.mtz, 3csl-rh-I.mtz, 3csl-ip-I.mtz) as well as mad_i.pdb and mad_i.phs (written by SHELXE) available from [ftp://{{SERVERNAME}}/pub/xds-datared/3csl/]. Furthermore the raw data can be downloaded there.

	=== additional information for those who want to complete the structure ===		=== additional information for those who want to complete the structure ===

Kay: /* additional information for those who want to complete the structure */

2014-05-19T14:14:21Z

additional information for those who want to complete the structure

← Older revision		Revision as of 16:14, 19 May 2014
Line 342:		Line 342:
	PELLAA		PELLAA
	</pre>		</pre>


			== See also ==
			GlobalPhasing autoproc wiki http://www.globalphasing.com/autoproc/wiki/index.cgi?ACA2011Tutorial3csl

			GlobalPhasing autoSHARP wiki http://www.globalphasing.com/sharp/wiki/index.cgi?ACA2011Tutorial3csl

Kay at 18:51, 4 August 2012

2012-08-04T18:51:46Z

← Older revision		Revision as of 20:51, 4 August 2012
Line 1:		Line 1:
	HasA/R (PDB id [http://www.pdb.org/pdb/explore/explore.do?structureId=3CSL 3CSL]) is a complex of a 22-stranded beta-barrel outer membrane protein (~~HAsR~~, 865 residues), its hemophore (HasA, 206 residues), and heme. The structure and its biological implications are described in "Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex" (Krieg, S., Huché, F., Diederichs, K., Izadi-Pruneyre, N., Lecroisey, A., Wandersman, C., Delepelaire, P., Welte, W. (2009), Proc. Nat. Acad. Sci. Vol. 106 pp. 1045-1050).		HasA/R (PDB id [http://www.pdb.org/pdb/explore/explore.do?structureId=3CSL 3CSL]) is a complex of a 22-stranded beta-barrel outer membrane protein (HasR, 865 residues), its hemophore (HasA, 206 residues), and heme. The structure and its biological implications are described in "Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex" (Krieg, S., Huché, F., Diederichs, K., Izadi-Pruneyre, N., Lecroisey, A., Wandersman, C., Delepelaire, P., Welte, W. (2009), Proc. Nat. Acad. Sci. Vol. 106 pp. 1045-1050).

	The ordered part of HasR has residues 112-865 and harbours 9 Met residues. The ordered part of HasA has 173 residues, one of which is Met - but that is mostly disordered, and was not Se-labelled. 3-wl SeMet-MAD data were collected at beamline X06SA of the SLS in November 2006 on a MarCCD detector.		The ordered part of HasR has residues 112-865 and harbours 9 Met residues. The ordered part of HasA has 173 residues, one of which is Met - but that is mostly disordered, and was not Se-labelled. 3-wl SeMet-MAD data were collected at beamline X06SA of the SLS in November 2006 on a MarCCD detector.
Line 321:		Line 321:
	== Availability of data ==		== Availability of data ==

	There are files with amplitudes (3csl-pk-F.mtz, 3csl-rh-F.mtz, 3csl-ip-F.mtz) and intensities (3csl-pk-I.mtz, 3csl-rh-I.mtz, 3csl-ip-I.mtz) as well as mad_i.pdb and mad_i.phs (written by SHELXE) available from [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/3csl/].		There are files with amplitudes (3csl-pk-F.mtz, 3csl-rh-F.mtz, 3csl-ip-F.mtz) and intensities (3csl-pk-I.mtz, 3csl-rh-I.mtz, 3csl-ip-I.mtz) as well as mad_i.pdb and mad_i.phs (written by SHELXE) available from [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/3csl/]. Furthermore the raw data can be downloaded there.

	=== additional information for those who want to complete the structure ===		=== additional information for those who want to complete the structure ===

Kay: change lins to raw data

2012-03-27T12:07:10Z

change lins to raw data

← Older revision		Revision as of 14:07, 27 March 2012
Line 28:		Line 28:

	=== Peak ===		=== Peak ===
	360 frames (0.5° oscillation) at the peak wavelength were collected after the high-remote data. They can be downloaded from [ftp://turn5.biologie.uni-konstanz.de/pub/~~datasets~~/3csl~~-pk.tar~~ here] (1.9 Gb). This peak dataset is somewhat difficult to index; if the results are really bad (e.g. distance refining far away from 370 mm) with the default 180 frames, then just try with 90 or 270 frames.		360 frames (0.5° oscillation) at the peak wavelength were collected after the high-remote data. They can be downloaded from [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/3csl/ here] (1.9 Gb). This peak dataset is somewhat difficult to index; if the results are really bad (e.g. distance refining far away from 370 mm) with the default 180 frames, then just try with 90 or 270 frames.

	This is an excerpt from [[CORRECT.LP]] :		This is an excerpt from [[CORRECT.LP]] :
Line 122:		Line 122:
	=== High-remote ===		=== High-remote ===

	Due to a beamline problem, high-remote data collection stopped after 269 frames of 0.5° (the final frame is already affected). After restart of the beamline, another 100 frames were collected but they later turned out to merge badly with the first 269 frames - a hint that the monochromator was still heating up, or similar. So the latter frames were left out. The 269 frames are [ftp://turn5.biologie.uni-konstanz.de/pub/~~datasets~~/3csl~~-hrem.tar~~ here] (1.4 Gb).		Due to a beamline problem, high-remote data collection stopped after 269 frames of 0.5° (the final frame is already affected). After restart of the beamline, another 100 frames were collected but they later turned out to merge badly with the first 269 frames - a hint that the monochromator was still heating up, or similar. So the latter frames were left out. The 269 frames are [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/3csl/ here] (1.4 Gb; you guessed that the file is called 3csl-hrem.tar, right?).

	From CORRECT.LP :		From CORRECT.LP :
Line 157:		Line 157:
	=== Inflection ===		=== Inflection ===

	360 frames (0.5° oscillation) at the inflection wavelength were collected after the peak data. They can be downloaded from [ftp://turn5.biologie.uni-konstanz.de/pub/~~datasets~~/3csl~~-ip.tar~~ here] (1.8 Gb).		360 frames (0.5° oscillation) at the inflection wavelength were collected after the peak data. They can be downloaded from [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/3csl/ here] (1.8 Gb).

	CORRECT.LP has:		CORRECT.LP has:

Kay at 11:07, 27 May 2011

2011-05-27T11:07:52Z

← Older revision		Revision as of 13:07, 27 May 2011
Line 1:		Line 1:
	HasA/R (PDB id [http://www.pdb.org/pdb/explore/explore.do?structureId=3CSL 3CSL]) is a complex of a 22-stranded beta-barrel outer membrane protein (HAsR, 865 residues), its hemophore (HasA, 206 residues), and heme. The structure and its biological implications are described in "Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex" (Krieg, S., Huché, F., Diederichs, K., Izadi-Pruneyre, N., Lecroisey, A., Wandersman, C., Delepelaire, P., Welte, W. (2009), Proc. Nat. Acad. Sci. Vol. 106 pp. 1045-1050.)		HasA/R (PDB id [http://www.pdb.org/pdb/explore/explore.do?structureId=3CSL 3CSL]) is a complex of a 22-stranded beta-barrel outer membrane protein (HAsR, 865 residues), its hemophore (HasA, 206 residues), and heme. The structure and its biological implications are described in "Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex" (Krieg, S., Huché, F., Diederichs, K., Izadi-Pruneyre, N., Lecroisey, A., Wandersman, C., Delepelaire, P., Welte, W. (2009), Proc. Nat. Acad. Sci. Vol. 106 pp. 1045-1050).

	3-wl SeMet-MAD data were collected at beamline X06SA of the SLS in November 2006 on a MarCCD detector. HasA/R crystallizes in spacegroup F222; cell parameters are a=157Å, b=163Å, c=596Å. There are 2 complexes per ASU. Data to about 3.0Å could be collected from this crystal, but the anomalous data are useful to about 5Å only. The ordered part of HasR has residues 112-865 and harbours 9 SeMet residues. The ordered part of HasA has 173 residues, one of which is Met - but that is mostly disordered, and was not Se-labelled. Altogether there are 1852 residues and two heme molecules in the ASU.

	These MAD data~~, giving~~ a structure with an average B of 100 Å<sup>2</sup>~~, constitute a~~ project ~~that~~ is challenging for humans, and currently too difficult for automatic methods of structure solution and model building. The deposited 3CSL structure was not obtained from these MAD data alone, but the model was actually refined against slightly better (2.7Å) data collected on a native crystal at the ESRF.		The ordered part of HasR has residues 112-865 and harbours 9 Met residues. The ordered part of HasA has 173 residues, one of which is Met - but that is mostly disordered, and was not Se-labelled. 3-wl SeMet-MAD data were collected at beamline X06SA of the SLS in November 2006 on a MarCCD detector.

			HasA/R crystallizes in spacegroup F222; cell parameters are a=157Å, b=163Å, c=596Å. There are 2 complexes per ASU. Data to about 3.0Å could be collected from one crystal, which was translated between wavelengths. The anomalous data are useful to about 5Å only. These MAD data correspond to a structure with an average B of 100 Å<sup>2</sup>; the project is challenging for humans, and currently too difficult for automatic methods of structure solution and model building.

			The deposited 3CSL structure was not obtained from these MAD data alone, but the model was actually refined against slightly better (2.7Å) data collected on a native crystal at the ESRF. Altogether there are 1852 residues and two heme molecules in the ASU.

Kay: /* Peak */

2011-05-26T19:39:57Z

Peak

← Older revision		Revision as of 21:39, 26 May 2011
Line 96:		Line 96:
	[[File:3csl-pk-beamdiv.png]]		[[File:3csl-pk-beamdiv.png]]

	Next, we can use xdsstat to get frame-wise statistics from XDS_ASCII.HKL:		Next, we can use [[xdsstat]] to get frame-wise statistics from XDS_ASCII.HKL:

	[[File:3csl-pk-xdsstat1.png]]		[[File:3csl-pk-xdsstat1.png]]

Kay: /* Scaling */

2011-05-26T19:39:03Z

Scaling

← Older revision		Revision as of 21:39, 26 May 2011
Line 208:		Line 208:
	1 3 36555 0.985 0.9971 0.2041		1 3 36555 0.985 0.9971 0.2041
	2 3 35630 0.989 1.0038 -0.0116		2 3 35630 0.989 1.0038 -0.0116
	These correlations are worse than what I like to see from MAD datasets. One might think that some of the badness is maybe due to the fact that we used an unrealistic high-resolution limit, but if we use INCLUDE_RESOLUTION_RANGE=50 32 (this has to given three times, after each of the INPUT_FILE lines) the correlations are exactly the same.		These correlations are worse than what I like to see from MAD datasets. One might think that some of the badness is maybe due to the fact that we used an unrealistic high-resolution limit, but if we use INCLUDE_RESOLUTION_RANGE=50 3.2 (this has to given three times, after each of the INPUT_FILE lines) the correlations are exactly the same.
	The file further reports CHI^2-VALUE OF FIT OF CORRECTION FACTORS around 1.15 which indicates that the scaling model is not entirely adequate, but it is unclear what to change, so we leave it at that (we could use STRICT_ABSORPTION_CORRECTION=TRUE to bring the number closer to 1).		The file further reports CHI^2-VALUE OF FIT OF CORRECTION FACTORS around 1.15 which indicates that the scaling model is not entirely adequate, but it is unclear what to change, so we leave it at that (we could use STRICT_ABSORPTION_CORRECTION=TRUE to bring the number closer to 1).

Kay at 14:52, 11 April 2011

2011-04-11T14:52:56Z

← Older revision		Revision as of 16:52, 11 April 2011
Line 1:		Line 1:
	HasA/R (PDB id [http://www.pdb.org/pdb/explore/explore.do?structureId=3CSL 3CSL]) is a complex of a 22-stranded beta-barrel outer membrane protein (HAsR, 865 residues), its hemophore (HasA, 206 residues), and heme. The structure and its biological implications are described in "Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex" (Krieg, S., Huché, F., Diederichs, K., Izadi-Pruneyre, N., Lecroisey, A., Wandersman, C., Delepelaire, P., Welte, W. (2009), Proc. Nat. Acad. Sci. Vol. 106 pp. 1045-1050.)		HasA/R (PDB id [http://www.pdb.org/pdb/explore/explore.do?structureId=3CSL 3CSL]) is a complex of a 22-stranded beta-barrel outer membrane protein (HAsR, 865 residues), its hemophore (HasA, 206 residues), and heme. The structure and its biological implications are described in "Heme uptake across the outer membrane as revealed by crystal structures of the receptor-hemophore complex" (Krieg, S., Huché, F., Diederichs, K., Izadi-Pruneyre, N., Lecroisey, A., Wandersman, C., Delepelaire, P., Welte, W. (2009), Proc. Nat. Acad. Sci. Vol. 106 pp. 1045-1050.)

	3-wl SeMet-MAD data were collected at beamline X06SA of the SLS in November 2006 on a MarCCD detector. HasA/R crystallizes in spacegroup F222; cell parameters are a=157Å, b=163Å, c=596Å. There are 2 complexes per ASU. Data to about 3.0Å could be collected from this crystal, but the anomalous data are useful to about 5Å only. The ordered part of HasR has residues 112-865 and harbours 9 SeMet residues. The ordered part of HasA has 173 residues, one of which is Met - but that is mostly disordered, and was not Se-labelled.		3-wl SeMet-MAD data were collected at beamline X06SA of the SLS in November 2006 on a MarCCD detector. HasA/R crystallizes in spacegroup F222; cell parameters are a=157Å, b=163Å, c=596Å. There are 2 complexes per ASU. Data to about 3.0Å could be collected from this crystal, but the anomalous data are useful to about 5Å only. The ordered part of HasR has residues 112-865 and harbours 9 SeMet residues. The ordered part of HasA has 173 residues, one of which is Met - but that is mostly disordered, and was not Se-labelled. Altogether there are 1852 residues and two heme molecules in the ASU.

	These MAD data, giving a structure with an average B of 100 Å<sup>2</sup>, constitute a project that is challenging for humans, and currently too difficult for automatic methods of structure solution and model building. The deposited 3CSL structure was not obtained from these MAD data alone, but the model was actually refined against slightly better (2.7Å) data collected on a native crystal at the ESRF.		These MAD data, giving a structure with an average B of 100 Å<sup>2</sup>, constitute a project that is challenging for humans, and currently too difficult for automatic methods of structure solution and model building. The deposited 3CSL structure was not obtained from these MAD data alone, but the model was actually refined against slightly better (2.7Å) data collected on a native crystal at the ESRF.