Quality Control

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This is an attempt of putting together a number of datasets with different characteristics (high and low resolution, good and bad crystals, untwinned and twinned), their evaluation with different versions of XDS up to the structure solution (as far as that can be done automatically), and the determination of the quality of the resulting data using experimental phasing and refinement.

Assorted projects

For each project mentioned below, both the raw data and the XDS data reduction is available - links are on the project pages, which are named according to their PDB ids.

The raw data (images) for the different datasets are either available from this site by FTP, or from the (publicly accessible!) JCSG dataset archive, or - for 1RQW - from [1] or [2].

There's currently data available for

  • 2-wl MAD: PDB id 1T92 (PulG, 116 residues, 2 copies/ASU, spacegroup P6522, resolution 2.8 Å)
  • 3-wl MAD: PDB id 1ZTV (JCSG target name TB1631F, resolution 3.1 Å) - evaluated with Qingping Xu; it's one of the JCSG datasets.
  • native data: PDB id 2GIF (AcrB, spacegroup C2, resolution 2.9 Å - a large membrane protein structure)
  • native data for MR: PDB id 1YCE (ATPase C-ring, spacegroup P21, resolution 2.4 Å - a large membrane protein structure, 44-fold NCS, strong diffuse scattering)
  • 2-wl Bromide MAD: PDB id 1RQW (Thaumatin, a sweet-tasting protein of 207 resides, spacegroup P41212, 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 Xray Tutorial).

ACA2011

As part of the 2011 ACA workshop on data processing, organized by Ed Collins and Andy Torelli, I extensively document XDS data processing (and in most cases also structure solution) of

  • 2VB1: 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 here. Details of data collection, processing and refinement are published.
  • simulated-1g1c: James Holton's simulated (using his MLFSOM program) data of PDB id 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 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. Datasets are at [3].
  • 3CSL: 3-wl SeMet-MAD data PDB id 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 [4]. 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.
  • 1Y13: SAD with a twist that requires some detective work.

ACA2014

Data from several projects were processed by experts at the "Data processing with the pros" session of the ACA2014 in Albuquerque, New Mexico (USA) at the end of May 2014. This website has detailed descriptions and links.

Simulated data

I wrote SIM_MX which makes testing and development of XDS independant from real data.