Table 1.
<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 ( |i − j| = 1) (962) | 0.029 ± 0.003 | 0.028 |
medium range (1 < |i − j| ≤1) (848) | 0.036 ± 0.003 | 0.035 |
long range ( |i − j| > 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 |
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.
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.
Lennard-Jones van der Waals energies were calculated using CHARMm parameters and were not used in any stage of the structure determination
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.
PROCHECK was utilized to generate the Ramachandran plot.
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.