validation of macromolecular structures: updating standards for publication of NMR structures in an IUCr journal

ACA 2007, Salt Lake City, Utah, USA

21 July 2007

Participants
Howard Einspahr, Acta Cryst. F
Mitchell Guss, Acta Cryst. F
Manfred Weiss, Acta Cryst. D
Luciano Mueller, Bristol-Myers Squibb
Rob Kaptein, Utrecht
Eldon Ulrich, BMRB
James Aramini, Rutgers
John Westbrook, RCSB
Clemens Anklin, Bruker BioSpin
Peter Strickland, IUCr Journals

Objective

The suggestion of having a workshop on standards for publication of NMR structures in IUCr journals was first discussed among D and F editors at the IUCr Commission on Journals Meeting in Montecatini, Italy in August 2005. With the publication of the first NMR structure in Acta Crystallographica Section F (Lytle et al., 2006), the need for a workshop became imperative. The objective of the workshop was to arrive at a list of data supplemental to the earlier IUPAC standards (Markley et al., 1998a, b, c) that are to be required or recommended for publication in any manuscript describing a three-dimensional macromolecular structure determined by NMR submitted to IUCr journals.


Summary of recommendations

1. The sample: The same rules and principles applied to the description of the preparation of the sample for X-ray crystal structure determination should be applied to the description of the preparation of the sample for NMR structure determination. For the description of specifically isotope-labeled samples, the rules laid out in chapter 1.6 'Isotope-labeled proteins and nucleic acids' of Markley et al. (1998a, b, c) apply.

2. The experiment: It was deemed very important to disclose all relevant experimental parameters as laid out in Section 5.1 of the IUPAC recommendations (Markley et al., 1998a, b, c). This does not necessarily need to be in the text, but may be supplied as Supplementary Information.

3. Data quality: Data quality is very difficult to judge for NMR. It is therefore required that authors provide a two-dimensional NMR spectrum, typically an assigned HSQC spectrum, of the sample under study either in the text or in the Supplementary Information. This requirement is already in effect for papers published in J. Biomol. NMR.

4. Structure quality: A table describing the overall quality of the structure should be supplied with the manuscript. This table should have the form of the table at the end of this document and should contain information on all the items. For all distributions, a mean and a standard deviation should be given. Whenever a number is reported on a reduced set of atoms or residues of a structure, this fragment must be defined in the footnote of the table. If the completeness of the assignment is less than 90%, an explanatory statement must be provided. For Table item Deviation from idealized geometry, a reference for ideal geometry has to be supplied. Additional global structure quality factors from software packages such as PSVS (Bhattacharya et al., 2007) may also be reported in the table (not required).

5. Definition of coordinates: Authors must describe how the ensemble of structures described in the manuscript was arrived at. They should specify how many total structures were calculated and which and how many out of this set of structures was used to assemble the ensemble. This can either be described in the Methods section of the paper or it may be provided in the table describing the overall structure quality (see point 4 above). Authors are also required to specify how the representative structure was chosen.

6. Agreement of the model with the experiment: In order to give the mainly crystallographic readership of Acta Crystallographica a feel for how good the NMR ensemble (or the representative structure) fits the experimental data, it is recommended (not required) to back-calculate NOEs from the model and provide a measure of the similarity of the observed and calculated lists. This is somewhat similar to the crystallographic R factor and could for instance be done using the program RPF (Huang et al., 2005).

7. Deposition of data: In addition to the coordinates, assigned chemical shifts and the restraint data used in the last round of refinement must be deposited with the PDB and BMRB. PDB and BMRB IDs are required at the stage of paper acceptance. BMRB will introduce a simple status checking system, similar to the one in the PDB. It is recommended that the NOE peak list also be the deposited.

8. Validation letters from PDB/BMRB: At the submission stage, the validation letters provided by the PDB and the BMRB should be supplied with the manuscript. They could for instance be attached to the manuscript so that they are available for review. They will not be published.

References

Bhattacharya, A., Tejero, R. & Montelione, G. T. (2007). Proteins, 66, 778-795. [CrossRef]
Huang, Y. J., Powers, R. & Montelione, G. T. (2005). J. Am. Chem. Soc. 127, 1665-1674. [CrossRef]
Lytle, B. L., Peterson, F. C., Tyler, E. M. , Newman, C. L., Vinarov, D. A., Markley, J. L. & Volkman, B. F. (2006). Acta Cryst. F62, 490-493. [details] [CrossRef]
Markley, J. L., Bax, A., Arata, Y., Hilbers, C. W. , Kaptein, R., Sykes, B. D., Wright, P. E. & Wüthrich, K. (1998a). J. Mol. Biol. 280, 933-952. [CrossRef]
Markley, J. L., Bax, A., Arata, Y., Hilbers, C. W., Kaptein, R., Sykes, B. D., Wright, P. E. & Wüthrich, K. (1998b). J. Biomol. NMR, 12, 1-23. [CrossRef]
Markley, J. L., Bax, A., Arata, Y., Hilbers, C. W., Kaptein, R., Sykes, B. D., Wright, P. E. & Wüthrich, K. (1998c). Eur. J. Biochem. 256, 1-15. [CrossRef]



Completeness of resonance assignments

Backbone
Side chain
Aromatic
Stereospecific methyl groups

Constraints


Non-redundant distance constraints

Total
Intraresidue (i = j)
Sequential (|i - j| = 1)
Medium range (1 < |i - j| < 5)
Long range (|i - j| ≥ 5)
Any intermolecular

Dihedral angle constraints (φ and ψ)

Hydrogen-bond constraints

Total constrained
Total constraints
Total long-range constraints (|i - j| ≥ 5)

Residual dipolar coupling (RDC) constraints (if applicable)

Total
Average per residue

Other kinds of constraints

Total number

Constraints per residue

Average number of constraints per residue

Constraint violations

Average number of distance constraint violations per structure

0.1-0.2 Å
0.2-0.5 Å
> 0.5 Å
Average r.m.s. distance violation per constraint (Å)
Maximum distance violation (Å)

Average number of dihedral angle violations per structure

1-10 °
> 10 °
Average r.m.s. dihedral angle violation per constraint (°)
Maximum dihedral angle violation (°)

Average atomic r.m.s.d. to the mean structure (Å)

For backbone atoms (N, Cα, C)
For all heavy atoms

Deviations from idealized covalent geometry

Bond length r.m.s.d. (Å)
Bond angle r.m.s.d. (°)

Lennard Jones energy (kJ mol-1)

Ramachandran statistics (% residues)

Most favored
Additionally allowed
Generously allowed
Disallowed