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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.
Huang, Y. J., Powers, R. & Montelione, G. T. (2005).
J. Am. Chem. Soc. 127, 1665-1674.
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.
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.
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.
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.
Completeness of resonance assignments
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Backbone
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Side chain
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Aromatic
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Stereospecific methyl groups
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Constraints
Non-redundant distance constraints |
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Total
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Intraresidue (i = j)
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Sequential (|i - j| = 1)
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Medium range (1 < |i - j| < 5)
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Long range (|i - j| ≥ 5)
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Any intermolecular
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Dihedral angle constraints (φ and ψ) |
Hydrogen-bond constraints |
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Total constrained
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Total constraints
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Total long-range constraints (|i - j| ≥ 5)
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Residual dipolar coupling (RDC) constraints (if applicable) |
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Total
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Average per residue
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Other kinds of constraints |
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Total number
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Constraints per residue |
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Average number of constraints per residue
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Constraint violations
Average number of distance constraint violations per structure |
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0.1-0.2 Å
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0.2-0.5 Å
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> 0.5 Å
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Average r.m.s. distance violation per constraint (Å)
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Maximum distance violation (Å)
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Average number of dihedral angle violations per structure |
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1-10 °
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> 10 °
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Average r.m.s. dihedral angle violation per constraint (°)
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Maximum dihedral angle violation (°)
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Average atomic r.m.s.d. to
the mean structure (Å)
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For backbone atoms (N, Cα, C)
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For all heavy atoms
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Deviations from idealized
covalent geometry
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Bond length r.m.s.d. (Å)
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Bond angle r.m.s.d. (°)
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Lennard Jones energy (kJ mol-1)
Ramachandran statistics (% residues)
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Most favored
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Additionally allowed
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Generously allowed
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Disallowed
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