xia2 Processing Report: nt5073v16
XIA2 version 0.3.6.3 completed with status 'normal termination'
Read output from /dls/i04-1/data/2014/nt5073-16/processed/BAZ2BA/BAZ2BA-x839/BAZ2BA-x839_2_/xia2/3daii-run
| SAD | ||
|---|---|---|
| Wavelength (Å) | 0.92000 | |
| High resolution limit | 2.04 | ( 9.12 - 2.04) |
| Low resolution limit | 37.14 | ( 37.14 - 2.09) |
| Completeness | 99.5 | ( 98.5 - 99.5) |
| Multiplicity | 6.5 | ( 6.1 - 6.9) |
| I/sigma | 14.1 | ( 42.8 - 2.6) |
| Rmerge | 0.073 | (0.028 - 0.604) |
| Anomalous completeness | 98.7 | ( 99.2 - 99.2) |
| Anomalous multiplicity | 3.3 | ( 3.8 - 3.4) |
| See all statistics | ||
| Unit cell dimensions: a (Å) | 83.500 | |
| b (Å) | 96.740 | |
| c (Å) | 57.970 | |
| α (°) | 90.000 | |
| β (°) | 90.000 | |
| γ (°) | 90.000 | |
| Spacegroup | C 2 2 21 | |
| Sfcheck twinning score | 2.39 Your data do not appear to be twinned | |
| All crystallographic parameters.. | ||
Contents of the rest of this document:
Crystallographic parameters
Unit cell
| a | b | c | α | β | &gamma |
|---|---|---|---|---|---|
| 83.500 | 96.740 | 57.970 | 90.000 | 90.000 | 90.000 |
The unit cell parameters are the average for all measurements
Spacegroup
Spacegroup: C 2 2 21
No likely alternatives to this spacegroup
The spacegroup was determined using pointless (see log file)
Twinning analysis
Overall twinning score: 2.39
Your data do not appear to be twinned
The twinning score is the value of <E4>/<I2> reported by sfcheck (see documentation)
Asymmetric unit contents
No information on ASU contents (because no sequence information was supplied?)
Output files
Reflection data files
xia2 produced the following reflection data files - to download, right-click on the link and select "Save Link As..."
| MTZ files | |
| Useful for: CCP4 and Phenix | |
| Dataset | File name |
| All datasets | nt5073v16_xBAZ2BAx8392_free.mtz |
| SCA files | |
| Useful for: AutoSHARP etc | |
| Dataset | File name |
| SAD | nt5073v16_xBAZ2BAx8392_scaled.sca |
| SCA_UNMERGED files | |
| Useful for: XPREP and Shelx C/D/E | |
| Dataset | File name |
| SAD | nt5073v16_xBAZ2BAx8392_scaled_unmerged.sca |
Log files
The log files are located in /dls/i04-1/data/2014/nt5073-16/processed/BAZ2BA/BAZ2BA-x839/BAZ2BA-x839_2_/xia2/3daii-run/LogFiles and are grouped by processing stage:
| Integration | |||
| Integration of each sweep | |||
| nt5073v16_xBAZ2BAx8392_SAD_SWEEP1_INTEGRATE.log | original | ||
| nt5073v16_xBAZ2BAx8392_SAD_SWEEP1_CORRECT.log | original | ||
| Spacegroup Determination | |||
| Decision making for the spacegroup assignment | |||
| nt5073v16_xBAZ2BAx8392_pointless.log | original | html |  See warnings |
| Scaling and merging | |||
| Scaling together all the data for this crystal | |||
| nt5073v16_xBAZ2BAx8392_XSCALE.log | original | ||
| Scaling and correction of all measurements on the crystal | |||
| nt5073v16_xBAZ2BAx8392_aimless.log | original | html | |
| Analysis | |||
| Intensity analysis for each wavelength of data | |||
| nt5073v16_xBAZ2BAx8392_SAD_truncate.log | original | html | |
The following files weren't assigned to a crystal:
Note to the xia2 developer: check the "addLogFile" definitions in the PipelineInfo class to ensure that information about these files exists and is correct.
xia2 Journal file
More detailed information on what xia2 did can be found in the "journal" file:
Integration status per image
The following sections show the status of each image from the final integration run performed on each sweep within each dataset.The table below summarises the image status for each dataset and sweep.
Dataset SAD
SWEEP1: batches 1 to 1800
Detailed statistics for each dataset
Detailed statistics for each dataset as reported by Scala
Dataset SAD
| Overall | Low | High | |
|---|---|---|---|
| High resolution limit | 2.04 | 9.12 | 2.04 |
| Low resolution limit | 37.14 | 37.14 | 2.09 |
| Completeness | 99.5 | 98.5 | 99.5 |
| Multiplicity | 6.5 | 6.1 | 6.9 |
| I/sigma | 14.1 | 42.8 | 2.6 |
| Rmerge | 0.073 | 0.028 | 0.604 |
| Rmeas(I) | 0.088 | 0.032 | 0.717 |
| Rmeas(I+/-) | 0.086 | 0.032 | 0.711 |
| Rpim(I) | 0.034 | 0.012 | 0.272 |
| Rpim(I+/-) | 0.045 | 0.016 | 0.371 |
| Wilson B factor | 24.212 | ||
| Anomalous completeness | 98.7 | 99.2 | 99.2 |
| Anomalous multiplicity | 3.3 | 3.8 | 3.4 |
| Anomalous correlation | 0.124 | -0.144 | 0.054 |
| Anomalous slope | 1.052 | 0.000 | 0.000 |
| dF/F | 0.073 | ||
| dI/s(dI) | 0.904 | ||
| Total observations | 99053 | 1246 | 7648 |
| Total unique | 15236 | 204 | 1115 |
Credits
Software used
- ccp4
- distl
- labelit
- pointless
- xds
- xia2
Citations
Note that links to external content below may require you to log in before you can view or download the materials
- (1994) Acta Crystallogr. D 50, 760--763
- Evans, Philip (2006) Acta Crystallographica Section D 62, 72--82
- Kabsch, Wolfgang (2010) Acta Crystallographica Section D 66, 125--132
- Sauter, Nicholas K. and Grosse-Kunstleve, Ralf W. and Adams, Paul D. (2004) Journal of Applied Crystallography 37, 399--409
- Winter, G. (2010) Journal of Applied Crystallography 43
- Zhang, Z. and Sauter, N.K. and van den Bedem, H. and Snell, G. and Deacon, A.M. (2006) J. Appl. Cryst 39, 112--119
xia2 Details
Details about this run:
| Version | 0.3.6.3 |
| Run time | 00h 06m 11s |
| Command line | xia2 -min_images 3 -3daii -xparallel -1 -atom s -blend -project nt5073v16 -crystal xBAZ2BAx8392 -ispyb_xml_out ispyb.xml -image /dls/i04-1/data/2014/nt5073-16/BAZ2BA/BAZ2BA-x839/BAZ2BA-x839_2_0001.cbf |
| Termination status | normal termination |
| xia2.txt file | /dls/i04-1/data/2014/nt5073-16/processed/BAZ2BA/BAZ2BA-x839/BAZ2BA-x839_2_/xia2/3daii-run/xia2.txt |