Newsletter 181 - 186 - 364
October 20, 2008 - January 12, 2009 - November 6, 2017

The NIH X-Ray Diffraction Interest Group

Newsletter web site:

Item 3: Topic Discussion


Alexander Wlodawer, Mi Li, Zbigniew Dauter: High-Resolution Cryo-EM Maps and Models: A Crystallographer's Perspective (PMID: 28867613)
The appearance of ten high-resolution cryoelectron microscopy (cryo-EM) maps of proteins, ribosomes, and viruses was compared with the experimentally phased crystallographic electron density maps of four proteins. We found that maps calculated at a similar resolution by the two techniques are quite comparable in their appearance, although cryo-EM maps, even when sharpened, seem to be a little less detailed. An analysis of models fitted to the cryo-EM maps indicated the presence of significant problems in almost all of them, including incorrect geometry, clashes between atoms, and discrepancies between the map density and the fitted models. In particular, the treatment of the atomic displacement (B) factors was meaningless in almost all analyzed cryo-EM models. Stricter cryo-EM structure deposition standards and their better enforcement are needed.

Mariusz Jaskolski: Pathological Behavior of Atomic Occupancy Factors

A number of PDB files have been detected and reported by Zbyszek Dauter, in which the atomic occupancy factors show a pathological behavior, where covalently connected atoms have uncorrelated fractional occupancies.  This pathology seems to have been spreading unnoticed because MR-generated structures inherited the pathology from some earlier models, and the refinement programs were not rigorous enough to block (or at least signal) the "infection".  You might be advised to check your PDB files for this pathology, using an ad-hoc server by Marcin Kowiel.

Mariusz Jaskolski (CBR): Ultra-High Resolution Structures in Validation

    Abstract: In variance with small-molecule crystallography, where structure refinement is highly overdetermined by a large surplus of diffraction data, the observation/parameter ratio in macromolecular crystallography is usually low and only at about 2.7-2.5 Å resolution reaches 1.0 for reasonably constructed models. It is, therefore, not only useful but mathematically necessary to use stereochemical restraints in macromolecular refinement at low resolution. At higher resolution the restraints are still used, for a variety of reasons, but at some point, usually when atomic resolution (1.2 Å) has been reached, they may be relaxed as the diffraction terms are "taking the refinement over". It is a valid question, however, if the restraints could be dropped altogether, and if yes, under what conditions. A separate question concerns the restraint targets themselves and the strictness with which they should be obeyed. The most popular library of stereochemical standards was compiled in 1991 by Engh and Huber from careful analysis of small-molecule structures available at that time in the Cambridge Structural Database (CSD). A survey of the entries deposited in the Protein Data Bank (PDB) indicates that often the models are forced to imitate the standards more closely than justified by the errors with which those standards were originally estimated. Additionally, with a nearly six-fold expansion of the CSD from 80,000 entries in 1991, it might be interesting to see if the "old" stereochemical standards are still valid. An even more interesting possibility is opened up by the explosive growth of the PDB (100-fold since 1990), now holding more than 52,000 entries, and especially by the rapid accumulation of ultra-high resolution protein structures. For example, 0.8 Å resolution macromolecular structures were unknown in 1997, while today there are about two dozen of them. Such structures are usually refined with utmost care and are only minimally "contaminated" by the prior knowledge enforced by stereochemical restraints. They offer, therefore, a unique possibility to review (and if necessary to adjust) the stereochemical standards of protein structure. A preliminary analysis indicates that while some of the "old" standards have withstood the test of time, some others might need small but clear adjustments. This is especially true of the peptide group, which can show higher deviations (up to 20º) from strict planarity than allowed by the restraints. It is also important conceptually that we are now able to obtain "protein parameters from proteins". With the currently attainable level of accuracy, one can investigate if there are any detectable idiosyncrasies of protein structure, related for instance to the specific nature of protein conformation or to specific interactions with the environment. Finally, the parameters derived from ultra-high resolution protein structures can serve not only as more appropriate stereochemical targets for model refinement but may also be used as validation criteria for lower resolution models. (Presentation)

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