Quality Control: Difference between revisions

Quality Control (view source)

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Kay

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 * native data for MR: PDB id [[1YCE]]  ([http://www.rcsb.org/pdb/explore.do?structureId=1YCE ATPase C-ring], spacegroup P2<sub>1</sub>, resolution 2.4 Å - a large membrane protein structure, 44-fold NCS, strong diffuse scattering)
 * 2-wl Bromide MAD: PDB id [[1RQW]] ([http://www.rcsb.org/pdb/explore.do?structureId=1RQW Thaumatin], a sweet-tasting protein of 207 resides, spacegroup P4<sub>1</sub>2<sub>1</sub>2, resolution 1.8 Å, collected at the DGK Workshop 2007; could also treat either peak or inflection as SAD. These datasets have been made available by Manfred S. Weiss and Annette Faust (see [http://www.embl-hamburg.de/Xray_Tutorial/ Xray Tutorial]).
-* S-SAD: PDB id [[2QVO]] ([http://www.rcsb.org/pdb/explore.do?structureId=2QVO AF1382], a 95-residue protein used by James Tucker Swindell II to establish optimized procedures for data reduction. The data available to solve the structure are two runs of 360° collected at 1.9Å wavelength.
-* 3-wl SeMet-MAD data PDB id [[3CSL]] ([http://www.pdb.org/pdb/explore/explore.do?structureId=3CSL 3CSL], a complex of a 22 stranded beta-barrel outer membrane protein (the ordered residues 112-865 harbour 9 SeMet), its 173-residue hemophore (1 SeMet), and heme. Datasets are at [ftp://turn5.biologie.uni-konstanz.de/pub/datasets/]. 2 complexes per ASU, useful data to 3.2Å, useful anomalous data to about 5Å. Challenging for humans, and too difficult for automatic methods of structure solution and model building.
-* hen egg-white lysozyme @ 0.65Å resolution, PDB id [[2VB1]]. Data (sweeps a to h, each comprising 60 to 360 frames of 72MB) were collected by Zbigniew Dauter at APS 19-ID and are available from [http://bl831.als.lbl.gov/example_data_sets/APS/19-ID/2vb1/ here]. Details of data collection, processing and refinement are [http://journals.iucr.org/d/issues/2007/12/00/be5097/index.html published].
+As part of the 2011 ACA workshop on data processing, organized by Ed Collins, I additionally document XDS data processing of
+* [[2VB1]]: hen egg-white lysozyme @ 0.65Å resolution, PDB id [http://www.rcsb.org/pdb/explore/explore.do?structureId=2VB1 2vb1]. Data (sweeps a to h, each comprising 60 to 360 frames of 72MB) were collected by Zbigniew Dauter at APS 19-ID and are available from [http://bl831.als.lbl.gov/example_data_sets/APS/19-ID/2vb1/ here]. Details of data collection, processing and refinement are [http://journals.iucr.org/d/issues/2007/12/00/be5097/index.html published].
+* [[simulated-1g1c]]: James Holton's simulated (using his MLFSOM) data of PDB id [http://www.rcsb.org/pdb/explore/explore.do?structureId=1G1C 1g1c] - 100 synthetic datasets (15 frames each) strongly affected by radiation damage. These 100 datasets were simulated in random orientations and with random (?) "crystal" sizes. The processing and scaling can be considered non-standard, and challenging.
+* [[2QVO]]: S-SAD: PDB id [http://www.rcsb.org/pdb/explore.do?structureId=2QVO AF1382], a 95-residue protein used by James Tucker Swindell II to establish optimized procedures for data reduction. The data available to solve the structure are two runs of 360° collected at 1.9Å wavelength.
+* [[3CSL]]: 3-wl SeMet-MAD data PDB id [http://www.pdb.org/pdb/explore/explore.do?structureId=3CSL 3CSL], a complex of a 22 stranded beta-barrel outer membrane protein (the ordered residues 112-865 harbour 9 SeMet), its 173-residue hemophore (1 SeMet), and heme. Datasets are at [ftp://turn5.biologie.uni-konstanz.de/pub/datasets/]. 2 complexes per ASU, useful data to 3.2Å, useful anomalous data to about 5Å. Challenging for humans, and too difficult for automatic methods of structure solution and model building.
 Recently I've written [[SIM_MX]] which should make parts of testing and development of XDS independant from real data.