Quality Control

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.

The goal of this is to find generally optimal parameters for XDS data reduction, to compare new versions of XDS with older ones, and to discover bugs or regressions. At the same time, it serves to display standard procedures for solving crystal structures, which may be used for teaching or learning crystallography.

The metrics I would like to look at is

• anomalous signal: SHELXC anomalous correlations (internally or between wavelengths); SHELXD (fixed version) success rates and CCall/CCweak maximum values. Clemens Vonrhein additionally suggested anomalous difference fourier peak heights.
• refinement of a given (known) set of heavy atom positions in (e.g.) SHARP (fixed version): r.m.s. or absolute phase difference, or map correlation w.r.t. phases from good model
• refinement with (e.g.) refmac5 (fixed version) of a given model, finding LL and R/R_free

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

• PDB id 1T92 (PulG, 2-wl MAD, spacegroup P6₅22, resolution 2.8 Å)
• PDB id 1ZTV (JCSG target name TB1631F, 3-wl MAD, resolution 3.1 Å) - evaluated with Qingping Xu; it's on of the JCSG datasets.
• PDB id 2GIF (AcrB, spacegroup C2, resolution 2.9 Å - a large membrane protein structure)
• PDB id 1YCE (ATPase C-ring, spacegroup P2₁, resolution 2.4 Å - a large membrane protein structure, 44-fold NCS, strong diffuse scattering)
• PDB id 1RQW (Thaumatin, a sweet-tasting protein of 207 resides, spacegroup P4₁2₁2, resolution 1.8 Å, collected at the DGK Workshop 2007; either as 2-wl MAD or treating either peak or inflection as SAD. These datasets have been made available by Manfred S. Weiss and Annette Faust (see Xray Tutorial).
• PDB id 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° of Sulfur-SAD data collected at 1.9Å wavelength.

Additionally, new data is available from Manfred Weiss which belongs to an updated version of the DGK Workshop. XDS data reduction was performed for thau_1, thau_2, hel_native, and hel_au.

Recently I've written SIM_MX which should make parts of testing and development of XDS independant from real data.