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. Author manuscript; available in PMC: 2010 Mar 13.
Published in final edited form as: J Mol Biol. 2009 Mar 13;386(5):1265–1277. doi: 10.1016/j.jmb.2009.01.022

Table 1.

NMR-derived restraints and statistics of 20 NMR structures1

<20> best
rmsd from distance constraints (Å)2
 total (3382) 0.037 ± 0.002 0.036
 intraresidue (570) 0.009 ± 0.004 0.010
 sequential ( |ij| = 1) (962) 0.029 ± 0.003 0.028
 medium range (1 < |ij| ≤1) (848) 0.036 ± 0.003 0.035
 long range ( |ij| > 5) (446) 0.045 ± 0.005 0.045
 intermolecular for dimer interface (130) 0.044 ± 0.006 0.034
 ambiguous intra- or inter- S100A1 subunit (38) 0.012 ± 0.010 0.005
 TRTK12 peptide (seq, med) (90) 0.028 ± 0.009 0.041
 Intermolecular S100A1 to TRTK12 peptide (96) 0.060 ± 0.011 0.062
 calcium ligand (18) 0.025 ± 0.010 0.029
 hydrogen bonds (184) 0.069 ± 0.005 0.064
rmsd from exptl dihedral constraints (°)
Φ,Ψ (276) 0.516 ± 0.120 0.502
rmsd from dipolar coupling restraints (Hz)
DNH (112) 1.652 ± 0.093 1.606
DCH (136) 3.296 ± 0.171 3.261
rmsd from exptl13C chemical shifts
13Cα (ppm) 1.261 ± 0.041 1.253
13Cβ (ppm) 1.054 ± 0.039 1.020
rmsd from idealized geometry
 bonds (Å) 0.006 ± 0.001 0.006
 angles (°) 0.978 ± 0.018 0.959
 impropers (°) 1.841 ± 0.010 1.844
Lennard-Jones potential energy (kcal/mol)3 −889 ± 28 −917
Q-factor4 0.26 ±0.04 0.25
% of residues in the most favorable region of the Ramachandran plot5 87.6 ± 2.4 91.3
Rmsd to the mean structure (Å)6
 all backbone atoms in S100A1 (3–88) 0.518 ± 0.088 0.339
 all heavy atoms in S100A1 (3–88) 1.097 ± 0.128 0.943
 all ordered backbone (S100A1 3–88, TRTK12 4–12) 0.565 ± 0.089 0.476
 all heavy atoms (S100A1 3–88, TRTK12 4–12) 1.118 ± 0.118 0.969
1

The 20 ensemble structures, <20>, are the results of simulated annealing calculations. The best structure is the closest to the average structure. The values shown for the <20> are the mean ± standard deviation.

2

All four subunits of the protein complex are included in all of these values. None of the 20 structures has a distance violation > 0.4 Å or a dihedral angle violation of > 5°. The force constants used in the SA calculations are as follows: 1000 kcal mol −1 Å2 for bond length, 500 kcal mol−1 rad−2 for angles and improper torsions, 4 kcal mol−1 Å−4 for the quartic van der Waals (vdw) repulsion term (hard-sphere effective vdw set to 0.8 times their values in CHARMm parameters), 50 kcal mole−1 Å−2 for experimental distance constraints, 100 kcal mol−1 Å−2 for non-crystallographic symmetry, 1kcal mol−1 Å−2 for distance symmetry constraints, 0.5 kcal mol−1 ppm−2 for the 13C chemical shift constraints, and 1.0 for the conformational database potential. The force constants (in kcal Hz−2) used for dipolar coupling restraints were as follows: 0.40 for 15N-1HN and 0.2 for 13Cα-1Hα.

3

Lennard-Jones van der Waals energies were calculated using CHARMm parameters and were not used in any stage of the structure determination

4

Q-values were determined by randomly removing 10% of all RDC values. To ensure accuracy, an ensemble of structures with a second randomly removed subset of RDCs was also run. The Q-value of this second set was 0.26.

5

PROCHECK was utilized to generate the Ramachandran plot.

6

Backbone calculations include Cα, N, and C′ atoms. Only residues 3–88 are included since no long-range NOE correlations were observed for residues 1–2 and 89–93 in S100A1 or residues 1–3 in the TRTK peptide.